JBrowse 2: a modular genome browser with views of synteny and structural variation

The genome sequence of the confused eyebright, Euphrasia confusa Pugsley

We present a genome assembly from a tetraploid specimen of the confused eyebright, Euphrasia confusa (Streptophyta; Magnoliopsida; Lamiales; Orobanchaceae). The genome sequence has a total length of 976.50 megabases. Most of the assembly is scaffolded into 22 chromosomal pseudomolecules, supporting the specimen being an allotetraploid (2 n = 4 x = 44). There are two mitochondrial genome scaffolds with lengths of 329.69 and 112.33 kilobases, and the plastid genome is 144.97 kilobases long.

The genome sequence of Tenthredo amoena Gravenhorst, 1807

We present a genome assembly from an individual female shiny-headed wasp-sawfly, Tenthredo amoena (Arthropoda; Insecta; Hymenoptera; Tenthredinidae). The genome sequence has a total length of 199.80 megabases. Most of the assembly (99.95%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 33.96 kilobases in length.

The genome sequence of the Dotted Oak Knot-horn moth, Phycita roborella (Denis & Schiffermüller) 1775

We present a genome assembly from an individual female Phycita roborella (the Dotted Oak Knot-horn moth; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence has a total length of 710.50 megabases. Most of the assembly is scaffolded into 33 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.32 kilobases in length.

The genome sequence of the Common Wainscot moth, Mythimna pallens Linnaeus, 1758

We present a genome assembly from an individual male Mythimna pallens (the Common Wainscot moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 719.10 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.33 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,343 protein-coding genes.

The genome sequence of the Shoulder-striped Wainscot moth, Leucania comma Linnaeus, 1761

We present a genome assembly from an individual female Leucania comma (the Shoulder-striped Wainscot moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence spans 751.70 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,477 protein-coding genes.

The genome sequence of a soliderfly, Stratiomys singularior (Harris, 1776)

We present a genome assembly from an individual female solidierfly, Stratiomys singularior (Arthropoda; Insecta; Diptera; Stratiomyidae). The genome sequence has a total length of 715.20 megabases. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 15.67 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,614 protein-coding genes.

The genome sequence of the Figwort Sawfly Tenthredo scrophulariae Linnaeus, 1758

We present a genome assembly from an individual male Tenthredo scrophulariae (Figwort Sawfly; Arthropoda; Insecta; Hymenoptera; Tenthredinidae). The genome sequence has a total length of 233.10 megabases. Most of the assembly (99.96%) is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 26.26 kilobases in length.

The genome sequence of the white-throated dipper, Cinclus cinclus (Linnaeus, 1758)

We present a genome assembly from a juvenile male Cinclus cinclus (the white-throated dipper; Chordata; Aves; Passeriformes; Cinclidae). The genome sequence has a total length of 1,170.80 megabases. Most of the assembly (93.88%) is scaffolded into 39 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 18.67 kilobases in length.

The genome sequence of a braconid wasp, Microplitis deprimator (Fabricius, 1798)

We present a genome assembly from an individual female braconid wasp, Microplitis deprimator (Arthropoda; Insecta; Hymenoptera; Braconidae). The genome sequence has a total length of 233.20 megabases. Most of the assembly (99.12%) is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.62 kilobases in length.

The genome sequence of an ichneumonid wasp, Pimpla contemplator (Muller, 1776)

We present a genome assembly from an individual male ichneumonid wasp, Pimpla contemplator (Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence has a total length of 270.30 megabases. Most of the assembly (92.24%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 27.79 kilobases in length.

The genome sequence of knotweed leaf beetle, Gastrophysa polygoni (Linnaeus, 1758)

We present a genome assembly from a female specimen of Gastrophysa polygoni (knotweed leaf beetle; Arthropoda; Insecta; Coleoptera; Chrysomelidae). The genome sequence has a total length of 369.80 megabases. Most of the assembly (99.89%) is scaffolded into 12 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.11 kilobases in length.

The genome sequence of a tachinid fly, Linnaemya vulpina (Fallén, 1810)

We present a genome assembly from an individual male tachinid fly, Linnaemya vulpina (Arthropoda; Insecta; Diptera; Tachinidae). The genome sequence has a total length of 554.00 megabases. Most of the assembly (98.85%) is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.72 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,599 protein-coding genes.

The genome sequence of the sardine, Sardina pilchardus (Walbaum, 1792)

We present a genome assembly from an individual Sardina pilchardus (the sardine; Chordata; Actinopteri; Clupeiformes; Clupeidae). The genome sequence spans 869.40 megabases. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.57 kilobases in length.

The genome sequence of the Black Medic, Medicago lupulina L

We present a genome assembly from a specimen of Black Medic, Medicago lupulina (Streptophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence has a total length of 575.40 megabases. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 294.12 kilobases and 123.99 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 27,424 protein-coding genes.

The genome sequence of the small nettle, Urtica urens L. (Urticaceae)

We present a genome assembly from a specimen of small nettle, Urtica urens (Streptophyta; Magnoliopsida; Rosales; Urticaceae). The genome sequence has a total length of 339.60 megabases. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 335.02 kilobases and 147.51 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 18,378 protein-coding genes.

A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study

BACKGROUND

The concept of pangenomics and the importance of structural variants is gaining recognition within the plant genomics community. Due to advancements in sequencing and computational technology, it has become feasible to sequence the entire genome of numerous individuals of a single species at a reasonable cost. Pangenomes have been constructed for many major diploid crops, including rice, maize, soybean, sorghum, pearl millet, peas, sunflower, grapes, and mustards. However, pangenomes for polyploid species are relatively scarce and are available in only few crops including wheat, cotton, rapeseed, and potatoes.

MAIN BODY

In this review, we explore the various methods used in crop pangenome development, discussing the challenges and implications of these techniques based on insights from published pangenome studies. We offer a systematic guide and discuss the tools available for constructing a pangenome and conducting downstream analyses. Alfalfa, a highly heterozygous, cross pollinated and autotetraploid forage crop species, is used as an example to discuss the concerns and challenges offered by polyploid crop species. We conducted a comparative analysis using linear and graph-based methods by constructing an alfalfa graph pangenome using three publicly available genome assemblies. To illustrate the intricacies captured by pangenome graphs for a complex crop genome, we used five different gene sequences and aligned them against the three graph-based pangenomes. The comparison of the three graph pangenome methods reveals notable variations in the genomic variation captured by each pipeline.

CONCLUSION

Pangenome resources are proving invaluable by offering insights into core and dispensable genes, novel gene discovery, and genome-wide patterns of variation. Developing user-friendly online portals for linear pangenome visualization has made these resources accessible to the broader scientific and breeding community. However, challenges remain with graph-based pangenomes including compatibility with other tools, extraction of sequence for regions of interest, and visualization of genetic variation captured in pangenome graphs. These issues necessitate further refinement of tools and pipelines to effectively address the complexities of polyploid, highly heterozygous, and cross-pollinated species.

The genome sequence of a woodlouse fly, Melanophora roralis (Linnaeus, 1758)

We present a genome assembly from an individual female woodlouse fly, Melanophora roralis (Arthropoda; Insecta; Diptera; Rhinophoridae). The genome sequence has a total length of 565.10 megabases. Most of the assembly (98.9%) is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 19.44 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,321 protein-coding genes.

The genome sequence of Hoary Whitlowgrass, Draba incana L

We present a genome assembly from a specimen of Draba incana (Streptophyta; Magnoliopsida; Brassicales; Brassicaceae). The genome sequence has a total length of 667.80 megabases. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules, supporting the specimen being an allotetraploid (2 n = 32). The mitochondrial and plastid genome assemblies have lengths of 283.08 kilobases and 153.57 kilobases, respectively.

The genome sequence of the alder spittlebug, Aphrophora alni (Fallén, 1805)

We present a genome assembly from an individual male Aphrophora alni (the alder spittlebug; Arthropoda; Insecta; Hemiptera; Aphrophoridae). The genome sequence has a total length of 1,781.50 megabases. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 27.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,940 protein-coding genes.

The genome sequence of the red-crested pochard, Netta rufina (Pallas, 1773)

We present a genome assembly from a female specimen of Netta rufina (the red-crested pochard; Chordata; Aves; Anseriformes; Anatidae). The genome sequence has a total length of 1,167.00 megabases. Most of the assembly (98.76%) is scaffolded into 42 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.62 kilobases in length.

The genome sequence of a hoverfly, Cheilosia grossa (Fallén, 1817)

We present a genome assembly from an individual male Cheilosia grossa (a hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence has a total length of 362.40 megabases. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.81 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,196 protein-coding genes.

SesamumGDB: a comprehensive platform for Sesamum genetics and genomics analysis

Sesame (Sesamum indicum L., 2n = 26) is a crucial oilseed crop cultivated worldwide. The ancient evolutionary position of the Sesamum genus highlights its value for genomics and molecular genetics research among the angiosperms of other genera. However, Sesamum is considered a small orphan genus with only a few genomic databases for cultivated sesame to date. The urgent need to construct comprehensive, curated genome databases that include genus-specific gene resources for both cultivated and wild Sesamum species is being recognized. In response, we developed Sesamum Genomics Database (SesamumGDB), a user-friendly genomic database that integrates extensive genomic resources from two cultivated sesame varieties (S. indicum) and seven wild Sesamum species, covering all three chromosome groups (2n = 26, 32, and 64). This database showcases a total of 352 471 genes, including 6026 related to lipid metabolism and 17 625 transcription factors within Sesamum. Equipped with an array of bioinformatics tools such as BLAST (basic local alignment search tool) and JBrowse (the Javascript browser), SesamumGDB facilitates data downloading, screening, visualization, and analysis. As the first centralized Sesamum genome database, SesamumGDB offers extensive insights into the genomics and genetics of sesame, potentially enhancing the molecular breeding of sesame and other oilseed crops in the future. Database URL: http://www.sgbdb.com/sgdb/.

The genome sequence of the pink-footed goose, Anser brachyrhynchus Baillon, 1834

We present a genome assembly from a female pink-footed goose, Anser brachyrhynchus (Chordata; Aves; Anseriformes; Anatidae). The genome sequence spans 1,287.30 megabases. Most of the assembly is scaffolded into 41 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 16.74 kilobases in length.

The genome sequence of a picture-winged fly, Melieria crassipennis (Fabricius, 1794)

We present a genome assembly from an individual female picture-winged fly, Melieria crassipennis (tArthropoda; Insecta; Diptera; Ulidiidae). The genome sequence has a total length of 414.00 megabases. Most of the assembly is scaffolded into 4 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.77 kilobases in length.

The genome sequence of a fungus weevil, Pseudeuparius sepicola (Fabricius, 1792)

We present a genome assembly from an individual male Pseudeuparius sepicola (Arthropoda; Insecta; Coleoptera; Anthribidae). The genome sequence has a total length of 769.10 megabases. Most of the assembly (99.99%) is scaffolded into 12 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 17.55 kilobases in length.

The genome sequence of black elder, Sambucus nigra Linnaeus, 1753 (Adoxaceae)

We present a genome assembly from an individual Sambucus nigra (the European elder; Streptophyta; Magnoliopsida; Dipsacales; Adoxaceae). The genome sequence has a total length of 11,813.70 megabases. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 724.11 kilobases and 158.06 kilobases, respectively.

The genome sequence of the Atlantic mackerel, Scomber scombrus Linnaeus, 1758

We present a genome assembly from an individual Scomber scombrus (the Atlantic mackerel; Chordata; Actinopteri; Scombriformes; Scombridae). The genome sequence has a total length of 764.10 megabases. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.56 kilobases in length.

The genome sequence of Inga oerstediana Benth

We present a genome assembly from an individual of Inga oerstediana (Streptophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence has a total length of 970.60 megabases. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 1,166.81 and 175.18 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 33,334 protein-coding genes.

The genome sequence of the planthopper, Conomelus anceps (Germar, 1821)

We present a genome assembly from an individual male Conomelus anceps (planthopper; Arthropoda; Insecta; Hemiptera; Delphacidae). The genome sequence has a total length of 957.80 megabases. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 21.98 kilobases in length.

The genome sequence of Inga leiocalycina Benth

We present a genome assembly from an individual of Inga leiocalycina (Streptophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence has a total length of 948.00 megabases. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules. The assembled mitochondrial genome sequences have lengths of 1,019.42 and 98.74 kilobases, and the plastid genome assembly is 175.51 kb long. Gene annotation of the nuclear genome assembly on Ensembl identified 33,457 protein-coding genes.

The genome sequence of fat-hen, Chenopodium album L

We present a genome assembly from an individual Chenopodium album (fat-hen; Streptophyta; Magnoliopsida; Caryophyllales; Chenopodiaceae). The genome sequence has a total length of 1,593.80 megabases. Most of the assembly (99.61%) is scaffolded into 27 chromosomal pseudomolecules suggesting the individual is an allohexaploid (2 n = 6 x = 54). The mitochondrial and plastid genome assemblies have lengths of 312.95 kilobases and 152.06 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 50,077 protein-coding genes.

The genome sequence of the hook-banded wasp hoverfly, Chrysotoxum festivum (Linnaeus, 1758)

We present a genome assembly from an individual female Chrysotoxum festivum (the hook-banded wasp hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence spans 870.80 megabases. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 18.45 kilobases in length.

The genome sequence of the Golden-tabbed robberfly, Eutolmus rufibarbis (Meigen, 1820)

We present a genome assembly from an individual female Golden-tabbed robberfly, Eutolmus rufibarbis (Arthropoda; Insecta; Diptera; Asilidae). The genome sequence has a total length of 285.90 megabases. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.22 kilobases in length.

High-quality chromosome-level genome assembly of female Artemia franciscana reveals sex chromosome and Hox gene organization

Artemia is a crustacean genus belonging to the order Anostraca in the class Branchiopoda and lives in inland hypersaline lakes. Among the genus, A. franciscana is a valuable species as a fish food in the aquaculture industry or as an aquatic model organism for toxicity tests. However, genomic data for A. franciscana remains incomplete. In this study, high-quality genome assembly at the chromosome level of female A. franciscana was conducted by combining various sequencing and assembly technologies. The final A. franciscana assembled genome was 1.27 Gb in length, containing 21 chromosomal scaffolds (>10 Mb). The scaffold N50 was 45.3 Mb, with a complete BUSCO value of 91.0 %, thereby confirming that a high-quality genome was assembled. Gene annotation shows that the A. franciscana genome contained 67.26 % of repetitive sequences, and a total of 26,923 protein-coding genes were predicted. Among the 21 chromosome-scale scaffolds, chromosome 1 was identified as a sex chromosome Z. Additionally, five contigs of putative W chromosome fragments and the candidate sex-determining genes were suggested. Ten homeobox (Hox) genes were identified in A. franciscana on the chromosome 14, which were in two subclusters with a large gap. Hox gene organizations within 13 arthropods showed that four anostracans had conserved synteny. This study provides a new female Artemia genome with sex chromosome and the first complete genomic arrangement of the Hox cluster in Anostraca. This study will be a useful genomic and genetic reference for understanding the evolution and development of A. franciscana.

The genome sequence of a lauxaniid fly, Tricholauxania praeusta (Fallén, 1820)

We present a genome assembly from an individual female Tricholauxania praeusta (a lauxaniid fly; Arthropoda; Insecta; Diptera; Lauxaniidae). The genome sequence has a total length of 661.30 megabases. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.31 kilobases in length. Gene annotation of this assembly on Ensembl identified 25,606 protein-coding genes.

eRNA-IDO: A One-stop Platform for Identification, Interactome Discovery, and Functional Annotation of Enhancer RNAs

Growing evidence supports the transcription of enhancer RNAs (eRNAs) and their important roles in gene regulation. However, their interactions with other biomolecules and their corresponding functionality remain poorly understood. In an attempt to facilitate mechanistic research, this study presents eRNA-IDO, the first integrative computational platform for the identification, interactome discovery, and functional annotation of human eRNAs. eRNA-IDO comprises two modules: eRNA-ID and eRNA-Anno. Functionally, eRNA-ID can identify eRNAs from de novo assembled transcriptomes. eRNA-ID includes eight kinds of enhancer makers, enabling users to customize enhancer regions flexibly and conveniently. In addition, eRNA-Anno provides cell-/tissue-specific functional annotation for both new and known eRNAs by analyzing the eRNA interactome from prebuilt or user-defined networks between eRNAs and protein-coding genes. The prebuilt networks include the Genotype-Tissue Expression (GTEx)-based co-expression networks in normal tissues, The Cancer Genome Atlas (TCGA)-based co-expression networks in cancer tissues, and omics-based eRNA-centric regulatory networks. eRNA-IDO can facilitate research on the biogenesis and functions of eRNAs. The eRNA-IDO server is freely available at http://bioinfo.szbl.ac.cn/eRNA_IDO/.

The genome sequence of the Large Red Damselfly Pyrrhosoma nymphula (Sulzer, 1776)

We present a genome assembly from an individual male Pyrrhosoma nymphula (the Large Red Damselfly; Arthropoda; Insecta; Odonata; Coenagrionidae). The genome sequence is 2,117.2 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.78 kilobases in length.

The genome sequence of lesser burdock, Arctium minus (Hill) Bernh. (Asteraceae)

We present a genome assembly of a diploid specimen of Arctium minus (lesser burdock; Tracheophyta; Magnoliopsida; Asterales; Asteraceae). The genome sequence is 1,903.1 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 312.58 kilobases and 152.71 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 27,734 protein-coding genes.

The genome sequence of a leaf beetle, Galeruca laticollis Sahlberg, C.R., 1838

We present a genome assembly from an individual leaf beetle, Galeruca laticollis (Arthropoda; Insecta; Coleoptera; Chrysomelidae). The genome sequence has a total length of 2,154.60 megabases. Most of the assembly (99.92%) is scaffolded into 12 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 19.98 kilobases in length. Gene annotation of this assembly on Ensembl identified 32,229 protein-coding genes.

The genome sequence of Langmaid's Yellow Underwing moth, Noctua janthina (Denis & Schiffermüller) 1775

We present a genome assembly from an individual male Noctua janthina (Langmaid's Yellow Underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 539.70 megabases. Most of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,089 protein-coding genes.

The genome sequence of the Long-tailed duck, Clangula hyemalis (Linnaeus, 1758)

We present a genome assembly from an individual male Clangula hyemalis (the Long-tailed duck; Chordata; Aves; Anseriformes; Anatidae). The genome sequence spans 1,206.10 megabases. Most of the assembly is scaffolded into 41 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.63 kilobases in length.

The genome sequence of the Sprawler moth, Asteroscopus sphinx Hufnagel, 1766

We present a genome assembly from an individual male Asteroscopus sphinx (the Sprawler moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 857.30 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z sex chromosome and a putative B chromosome. The mitochondrial genome has also been assembled and is 15.35 kilobases in length.

The genome sequence of common reed, Phragmites australis (Cav.) Steud. (Poaceae)

We present a genome assembly from an individual Phragmites australis (the common reed; Streptophyta; Magnoliopsida; Poales; Poaceae). The genome sequence has a total length of 848.70 megabases. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules, supporting the specimen being an allotetraploid (2 n = 4 x = 48). The three mitochondrial assemblies had lengths of 304.58, 92.24, and 76.54 kilobases and the plastid genome assembly had a length of 137.67 kilobases. Gene annotation of this assembly on Ensembl identified 47,513 protein-coding genes.

The genome sequence of the Orange-tipped sea squirt, Corella eumyota Traustedt, 1882

We present a genome assembly from an individual specimen of Corella eumyota (the Orange-tipped sea squirt; Chordata; Ascidiacea; Phlebobranchia; Corellidae). The genome sequence is 129.3 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 14.53 kilobases in length.

The genome sequence of the Satin Lutestring moth, Tetheella fluctuosa (Hübner, 1803)

We present a genome assembly from an individual female Tetheella fluctuosa (the Satin Lutestring moth; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence has a total length of 369.10 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.41 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,318 protein-coding genes.

The genome sequence of the white-tailed eagle, Haliaeetus albicilla (Linnaeus, 1758)

We present a genome assembly from an individual female Haliaeetus albicilla (the white-tailed eagle; Chordata; Aves; Accipitriformes; Accipitridae). The genome sequence has a total length of 1,320.30 megabases. Most of the assembly is scaffolded into 34 chromosomal pseudomolecules, including the Z and W sex chromosomes. Gene annotation of this assembly on Ensembl identified 17,501 protein-coding genes.

Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective, Darwin Tree of Life Consortium. The genome sequence of the giant tachinid fly, Tachina grossa (Linnaeus, 1758)

We present a genome assembly from an individual female Tachina grossa (the giant tachinid fly; Arthropoda; Insecta; Diptera; Tachinidae). The genome sequence spans 936.90 megabases. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.82 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,428 protein-coding genes.

Functional and regulatory diversification of Period genes responsible for circadian rhythm in vertebrates

The Period genes (Per) play essential roles in modulating the molecular circadian clock timing in a broad range of species, which regulates the physiological and cellular rhythms through the transcription-translation feedback loop. While the Period gene paralogs are widely observed among vertebrates, the evolutionary history and the functional diversification of Per genes across vertebrates are not well known. In this study, we comprehensively investigated the evolution of Per genes at the copy number and sequence levels, including de novo binding motif discovery by comparative genomics. We also determined the lineage-specific transcriptome landscape across tissues and developmental stages and phenotypic effects in public RNA-seq data sets of model species. We observed multiple lineage-specific gain and loss events Per genes, though no simple association was observed between ecological factors and Per gene numbers in each species. Among salmonid fish species, the per3 gene has been lost in the majority, whereas those retaining the per3 gene exhibit not a signature of relaxed selective constraint but rather a signature of intensified selection. We also determined the signature of adaptive diversification of the CRY-binding region in Per1 and Per3, which modulates the circadian rhythm. We also discovered putative regulatory sequences, which are lineage-specific, suggesting that these cis-regulatory elements may have evolved rapidly and divergently across different lineages. Collectively, our findings revealed the evolution of Per genes and their fine-tuned contribution to the plastic and precise regulation of circadian rhythms in various vertebrate taxa.

The genome sequence of Inga laurina (Sw.) Willd

We present a genome assembly from an individual of Inga laurina (Streptophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence has a total length of 899.60 megabases. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules, supporting the individual being an autotetraploid with 2 n=4 x=52. The mitochondrial and plastid genome assemblies have lengths of 1,261.88 kilobases and 176.27 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 33,101 protein-coding genes.

The genome sequence of the Heart and Dart moth, Agrotis exclamationis (Linnaeus, 1758)

We present a genome assembly from an individual female Heart and Dart moth, Agrotis exclamationis (Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 725.10 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,008 protein-coding genes.