Comparative genomics · statistical methods · animal genetics

Jiaqi Wu 呉 佳齊 · ウー・ジャーチー

Assistant Professor, Hiroshima University
Graduate School of Integrated Sciences for Life & School of Applied Biological Science (Applied Animal & Plant Science) · Higashi-Hiroshima, Japan

I study how traits, breeding, and adaptation arise from large-scale genomic data across mammals, poultry and livestock, wild animals, and viruses — and I build methods that make large-scale comparative genomic analysis comparable and reproducible, so that the same branch really is being compared across genes.

01

About

I am an evolutionary genomicist in the Applied Animal and Plant Science program at Hiroshima University's School of Applied Biological Science, where I teach animal genetics and breeding. I work at the intersection of comparative genomics, molecular evolution, statistical genetics, and bioinformatics, extracting shared evolutionary principles from large-scale genomic data across mammals, birds and poultry, livestock, insects, and viruses.

A recurring theme in my work is whether large-scale analyses are really comparing the same evolutionary object — and building the methods, benchmarks, and reproducible workflows that make sure they are. Trained in medicine (BS, Shandong University), bioinformatics (MS, Fudan University, with the late Prof. Yang Zhong and Prof. Masami Hasegawa), and statistical genetics (PhD, The University of Tokyo, with Prof. Hirohisa Kishino), I have since held positions at Tokyo Institute of Technology (JSPS Research Fellow), Tokai University School of Medicine (JST CREST), and Hiroshima University.

To me, animal-breeding genomics and evolutionary genomics are one framework, not two. The same statistical-genomics toolkit that dates mammalian life-history evolution also speaks to poultry and livestock breeding — the origins, population structure, and diversity of native chickens and goats — and to the genomic monitoring of wild mammals for conservation and population management, as in my work on the Asian black bear, Japanese wolves, and bats. I connect the deep history of species divergence with within-species and within-breed diversity, adaptation, and selection on a common footing.

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Research

From animal genetics and breeding to method development — connecting the deep history of species divergence with within-breed diversity, adaptation, and selection on a common, auditable footing.

Phylogenomic methods

Branch comparability across genes

When taxa are missing or gene trees disagree, distinct species-tree branches can collapse or vanish. I develop split-based coordinate systems that make branch identity — and every kind of absence — explicit and reproducible.

Molecular evolution

Rates, life history & constraint

Molecular evolutionary rate as a window on mammalian life-history evolution, functional constraint, and intraspecific polymorphism — including a proposed post-K–Pg nocturnal bottleneck of placental mammals.

Viral genomics

Genome surveillance & variant dynamics

Design and analysis of viral genome-variation databases for the Genotype-to-Phenotype Japan (G2P-Japan) consortium — SARS-CoV-2 variant emergence and spread, plus HCV drug-resistance and KSHV transmission.

Animal genetics & breeding

Poultry, livestock & wild mammals

Population and comparative genomics for breeding and conservation — origins and structure of native chickens and goats, and genomic monitoring of wild mammals (Asian black bear, Japanese wolves, bats), extending to silkworm, noctuid pests, ratite birds, and beyond.

Current focus — SplitAligner

A branch-identity coordinate system for phylogenomics under missing taxa and gene-tree discordance. It defines branch identity through projected species-tree splits and decomposes branch absence into explicit, auditable categories, with a deterministic graph-oracle benchmark (Catnip10) and an R implementation with a C++ core (SplitAlignerR). Its branch coordinates are defined by canonical unrooted splits rather than display-root or positional node identities, so equivalent representations of the same weighted unrooted tree preserve the same biological branch identities.

Current focus — Catnip10

A deterministic 10-tip conformance benchmark for branch-wise workflows that file values on a fixed or shared reference-branch axis. An independent graph oracle supplies the truth object, and a workflow is scored on two axes: pruning-aware coordinate eligibility, and representation-stable coordinate identity and availability. SplitAligner builds coordinates; Catnip10 tests them.

03

Software

Open-source tools I develop and maintain. Methods, validation data, and reproducible workflows are released together.

SplitAligner

Perlphylogenomics2026

A branch-identity coordinate system that maps each gene tree onto species-tree splits under a locus's own taxon coverage, and names every kind of branch absence (structural, fusion, topology-induced). Ships the deterministic Catnip10 audit benchmark.

Catnip10

Python / RMITconformance benchmark

A deterministic ten-tip conformance benchmark for branch-wise workflows that file values on a fixed or shared reference-branch axis. An independent graph-contraction oracle supplies the truth object, and workflows are scored on two axes: pruning-aware coordinate eligibility, and representation-stable coordinate identity. Developed within the SplitAligner validation ecosystem.

SplitAlignerR

R / C++17GPL-3v0.1.0 · Pro RECERT certified

The R interface and independent benchmark track for SplitAligner. v0.1.0 ships a production C++17 graph-first mapper with strict finite-range branch-length validation, explicit structural and topological states, and composite-coordinate provenance; a separate paired fixed/free finalization layer that keeps literal NA as residual NA; and a pure R node-edge oracle that independently recomputes the whole Catnip10 benchmark (272 cells, 19 fusion events). The immutable v0.1.0 release passed independent Pro RECERT; the default branch is the post-release development line.

La Terra

RMIT2026in development

A matrix-first R framework for branch-wise comparative genomics. Starting from a SplitAlignerR exchange (gene × branch matrix, species tree, branch-coordinate keys, cell states and provenance), it brings gene-level trait-association screens, sparse predictive models with grouped validation, and diagnostic plots into one traceable workflow. The current release supports binary traits and installs against a pinned SplitAlignerR backend prerelease (0.1.0.9002, SHA-256 verified) so that results stay reproducible while both packages evolve.

SGV-Caller

PerlMIT2025

A SARS-CoV-2 genome-variation caller that builds local variation databases at nucleotide, codon, and amino-acid levels from GISAID data. Developed for the G2P-Japan consortium as an underlying data source for monitoring viral variants in Japan.

RRAA

Perl2025population genetics

Reduced-Representation Admixture Analysis. A Perl pipeline that tests how inbreeding within a target population affects the stability of population structure inferred by ADMIXTURE: it repeatedly subsamples individuals from that population, reruns ADMIXTURE at a chosen K, and summarises how the assignments move. Built on vcftools and ADMIXTURE; ships a goat SNP example dataset.

04

Publications

Selected peer-reviewed articles; full list on Google Scholar ↗.

2026
2025
2024
2023
  • 13Multiple mutations of SARS-CoV-2 Omicron BA.2 orchestrate its virological characteristicsCo-first
    Kimura I, Yamasoba D, Nasser H, Ito H, Zahradnik J, Wu J, Fujita S, Uriu K, … Sato K. 2023. Journal of Virology 97(10):e0101123.
  • 14Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants
    Tamura T, Ito J, Uriu K, … Genotype to Phenotype Japan Consortium (Wu J), … Sato K. 2023. Nature Communications 14(1):2800.
  • 15Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1
    Ito J, Suzuki R, Uriu K, … Genotype to Phenotype Japan Consortium (Wu J), … Sato K. 2023. Nature Communications 14(1):2671.
  • 16SARS-CoV-2 Haplograph: visualization of SARS-CoV-2 haplotype spread in Japan
    Nakagawa S, Katayama T, Jin L, Wu J, Kryukov K, Oyachi R, et al.. 2023. Genes & Genetic Systems 98(5):221.
2022
  • 17Molecular evolutionary rate predicts intraspecific genetic polymorphism and species-specific selectionCorresponding
    Wu J, Yonezawa T, Kishino H. 2022. Genes 13(4):708.
  • 18Massive loss of transcription factors promotes the initial diversification of placental mammalsCo-first
    Zhao X, Wu J, Kishino H, Chen L. 2022. International Journal of Molecular Sciences 23(17):9720.
  • 19The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistanceCo-first
    Kimura I, Kosugi Y, Wu J, Zahradnik J, … Sato K. 2022. Cell Reports 38:110218.
  • 20SARS-CoV-2 spike P681R mutation, a hallmark of the Delta variant, enhances fusogenicity and pathogenicity
    Saito A, Irie T, Suzuki R, … Wu J, … Kawaoka Y, Sato K. 2022. Nature 602:300.
  • 21Attenuated fusogenicity and pathogenicity of the SARS-CoV-2 Omicron variant
    Suzuki R, Yamasoba D, Kimura I, … Genotype to Phenotype Japan (Wu J), … Sato K. 2022. Nature 603:700.
  • 22Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity
    Meng B, Abdullahi A, … Genotype to Phenotype Japan Consortium (Wu J), … Gupta RK. 2022. Nature 603:706.
  • 23Paleogenomics reveals independent and hybrid origins of two wolf lineages endemic to Japan
    Segawa T, Yonezawa T, Mori H, … Wu J, … Nishihara H. 2022. Current Biology 32(11):2494.
2021
  • 24Evolution of reproductive life history in mammals and the associated change of functional constraintsCorresponding
    Wu J, Yonezawa T, Kishino H. 2021. Genes 12(5):740.
  • 25World-wide prevalence of substitutions in the HCV genome associated with resistance to direct-acting antiviralsCo-first
    Liu Z, Mao X, Wu J, Yu K, … Chen X. 2021. Clinical Gastroenterology and Hepatology 19:1906.
  • 26SARS-CoV-2 B.1.617.2 (Delta) variant replication and immune evasion
    Mlcochova P, Kemp SA, … Genotype to Phenotype Japan Consortium (Wu J), … Gupta RK. 2021. Nature 599:114.
  • 27SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity
    Motozono C, Toyoda M, … Genotype to Phenotype Japan Consortium (Wu J), … Sato K. 2021. Cell Host & Microbe 29:1124.
2020
  • 28Comparative genomic analyses illuminate the distinct evolution of megabats within Chiroptera
    Nikaido M, Kondo S, Zhang Z, Wu J, … Kai C. 2020. DNA Research 27:1.
2018
  • 29A single pheromone receptor gene conserved across 400 My of vertebrate evolution
    Suzuki H, Nishida H, … Wu J, … Nikaido M. 2018. Molecular Biology and Evolution 35:2928.
2017
  • 30Rates of molecular evolution suggest natural history of life-history traits and a post-K–Pg nocturnal bottleneck of placentalsCorresponding
    Wu J, Yonezawa T, Kishino H. 2017. Current Biology 27:3025.
  • 31Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pestCo-first
    Cheng T, Wu J, Wu Y, … Goldsmith MR, Feng Q, Xia Q, Mita K. 2017. Nature Ecology & Evolution 1:1747.
  • 32Phylogenomics and morphology of extinct paleognaths reveal the origin and evolution of the ratites
    Yonezawa T, Segawa T, … Wu J, … Willerslev E, Hasegawa M. 2017. Current Biology 27:68.
  • 33Expression map of a complete set of gustatory receptor genes in chemosensory organs of Bombyx mori
    Guo H, Cheng T, … Wu J, … Xia Q, Mita K. 2017. Insect Biochemistry and Molecular Biology 82:74.
2015
  • 34Phylogeographic and demographic analysis of the Asian black bear (Ursus thibetanus) based on mitochondrial DNAFirst author
    Wu J, Kohno N, Mano S, Fukumoto Y, Tanabe H, Hasegawa M, Yonezawa T. 2015. PLoS ONE 10:e0136398.
2014
  • 35Importance of synonymous substitutions under dense taxon sampling and appropriate modeling in reconstructing the mitogenomic tree of EutheriaFirst author
    Wu J, Hasegawa M, Zhong Y, Yonezawa T. 2014. Genes & Genetic Systems 89:237.
2013
  • 36High-altitude adaptation of the schizothoracine fishes (Cyprinidae) revealed by mitochondrial genome analyses
    Li Y, Ren Z, Shedlock AM, Wu J, … Yonezawa T, Zhong Y. 2013. Gene 517:169.
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Contact

I welcome collaborations across comparative genomics, molecular evolution, statistical genetics, and bioinformatics — from method development and benchmarking to real-data analysis in animals, viruses, and beyond.