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1. Liftoff: accurate mapping of gene annotations

   https://doi.org/10.1093/bioinformatics/btaa1016  

   Shumate, Alaina; Salzberg, Steven L (May 2021, Bioinformatics)

   Valencia, Alfonso (Ed.)

   Abstract Motivation Improvements in DNA sequencing technology and computational methods have led to a substantial increase in the creation of high-quality genome assemblies of many species. To understand the biology of these genomes, annotation of gene features and other functional elements is essential; however, for most species, only the reference genome is well-annotated. Results One strategy to annotate new or improved genome assemblies is to map or ‘lift over’ the genes from a previously annotated reference genome. Here, we describe Liftoff, a new genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely related species. Liftoff aligns genes from a reference genome to a target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript and gene. We show that Liftoff can accurately map 99.9% of genes between two versions of the human reference genome with an average sequence identity >99.9%. We also show that Liftoff can map genes across species by successfully lifting over 98.3% of human protein-coding genes to a chimpanzee genome assembly with 98.2% sequence identity. Availability and implementation Liftoff can be installed via bioconda and PyPI. In addition, the source code for Liftoff is available at https://github.com/agshumate/Liftoff. Supplementary information Supplementary data are available at Bioinformatics online. 

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2. Manual annotation of Drosophila genes: a Genomics Education Partnership protocol

   https://doi.org/10.12688/f1000research.126839.2  

   Rele, Chinmay P.; Sandlin, Katie M.; Leung, Wilson; Reed, Laura K. (January 2022, F1000Research)

   Annotating the genomes of multiple species allows us to analyze the evolution of their genes. While many eukaryotic genome assemblies already include computational gene predictions, these predictions can benefit from review and refinement through manual gene annotation. The Genomics Education Partnership (GEP; https://thegep.org/ ) developed a structural annotation protocol for protein-coding genes that enables undergraduate student and faculty researchers to create high-quality gene annotations that can be utilized in subsequent scientific investigations. For example, this protocol has been utilized by the GEP faculty to engage undergraduate students in the comparative annotation of genes involved in the insulin signaling pathway in 27 Drosophila species, using D. melanogaster as the reference genome. Students construct gene models using multiple lines of computational and empirical evidence including expression data (e.g., RNA-Seq), sequence similarity (e.g., BLAST and multiple sequence alignment), and computational gene predictions. Quality control measures require each gene be annotated by at least two students working independently, followed by reconciliation of the submitted gene models by a more experienced student. This article provides an overview of the annotation protocol and describes how discrepancies in student submitted gene models are resolved to produce a final, high-quality gene set suitable for subsequent analyses. The protocol can be adapted to other scientific questions (e.g., expansion of the Drosophila Muller F element) and species (e.g., parasitoid wasps) to provide additional opportunities for undergraduate students to participate in genomics research. These student annotation efforts can substantially improve the quality of gene annotations in publicly available genomic databases. 

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3. A new chromosome-level genome assembly for western painted turtle Chrysemys picta belli, a model for extreme physiological adaptations

   https://doi.org/10.1101/2025.04.01.646645  

   Chen, Junhao; Bermingham, John R; Minx, Patrick; Kremitzky, Milinn; Lin, Zhenguo; Warren, Daniel E (April 2025, bioRxiv)

   The western painted turtle, Chrysemys picta bellii, has the greatest tolerance to anoxia of any tetrapod studied to date. These turtles reside in the northern United States and southern Canada, and survive months of anoxia while submerged in ice-locked ponds and bogs. Reference genomes provide an important resource for elucidating the molecular bases for such unique physiological traits. An initial reference genome for this species was published in 2013, but the assembly is highly fragmented which poses several limitations for downstream analyses and biological interpretation. In this study, we created a new and improved assembly by combining PacBio HiFi, 10x Genomics Chromium, Hi-C sequence data and BioNano optical mapping derived from a single individual to generate a new haplotype-resolved chromosome-level assembly for C. picta bellii, called SLU_Cpb5.0. The genome size of the primary assembly is 2.372 Gb with a scaffold N50 of 133.6 Mb, which is a 6.5-fold improvement over the existing assembly. Genome annotation of SLU_Cpb5.0 revealed 12,242 novel genes compared to previous assemblies. Our PacBio Iso-Seq RNA sequencing data for twelve tissues unraveled over 100,000 novel transcript isoforms and 4,325 novel genes that were not annotated by standard NCBI pipeline. We also observed distinct patterns of tissue-specific isoform expression, creating a robust foundation for future characterization of the functions of these genes. The improved genome assembly and annotation will facilitate comparative genomics studies to better understand the genetic basis of C.picta bellii's extreme physiological adaptations and other aspects of its biology. 

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4. The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual

   https://doi.org/10.1093/g3journal/jkac321  

   Chao, Kuan-Hao; Zimin, Aleksey V.; Pertea, Mihaela; Salzberg, Steven L.; Emerson, ed., J. J. (January 2023, G3: Genes, Genomes, Genetics)

   Abstract We used long-read DNA sequencing to assemble the genome of a Southern Han Chinese male. We organized the sequence into chromosomes and filled in gaps using the recently completed T2T-CHM13 genome as a guide, yielding a gap-free genome, Han1, containing 3,099,707,698 bases. Using the T2T-CHM13 annotation as a reference, we mapped all genes onto the Han1 genome and identified additional gene copies, generating a total of 60,708 putative genes, of which 20,003 are protein-coding. A comprehensive comparison between the genes revealed that 235 protein-coding genes were substantially different between the individuals, with frameshifts or truncations affecting the protein-coding sequence. Most of these were heterozygous variants in which one gene copy was unaffected. This represents the first gene-level comparison between two finished, annotated individual human genomes. 

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5. A haplotype-resolved reference genome for Eucalyptus grandis

   https://doi.org/10.1093/g3journal/jkaf112  

   Lötter, Anneri; Bruna, Tomas; Duong, Tuan A; Barry, Kerrie; Lipzen, Anna; Daum, Chris; Yoshinaga, Yuko; Grimwood, Jane; Jenkins, Jerry W; Talag, Jayson; et al (May 2025, G3: Genes, Genomes, Genetics)

   Ingvarsson, P (Ed.)

   Abstract Eucalyptus grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials, and biorefinery products. The current v2.0 genome reference for the species served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts. Using PacBio HiFi long reads and Omni-C proximity ligation sequencing, we produced an improved, haplotype-phased assembly (v4.0) for TAG0014, an early-generation selection of E. grandis. The 2 haplotypes are 571 Mbp (HAP1) and 552 Mbp (HAP2) in size and consist of 37 and 46 contigs scaffolded onto 11 chromosomes (contig N50 of 28.9 and 16.7 Mbp), respectively. These haplotype assemblies are 70–90 Mbp smaller than the diploid v2.0 assembly but capture all except one of the 22 telomeres, suggesting that substantial redundant sequence was included in the previous assembly. A total of 35,929 (HAP1) and 35,583 (HAP2) gene models were annotated, of which 438 and 472 contain long introns (>10 kbp) in gene models previously (v2.0) identified as multiple smaller genes. These and other improvements have increased gene annotation completeness levels from 93.8 to 99.4% in the v4.0 assembly. We found that 6,493 and 6,346 genes are within tandem duplicate arrays (HAP1 and HAP2, respectively, 18.4 and 17.8% of the total) and >43.8% of the haplotype assemblies consists of repeat elements. Analysis of synteny between the haplotypes and the E. grandis v2.0 reference genome revealed extensive regions of collinearity, but also some major rearrangements, and provided a preview of population and pangenome variation in the species. 

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