preprint

An acidophilic fungus is integral to prey digestion in a carnivorous plant
PF Sun, MR Lu, YC Liu, YF Lin, DZ Hoh, HM Ke, IF Wang, MEJ Lu, R Kirschner, YCJ Lin, YL Chen and IJ Tsai.

Genomes of keystone Mortierella species lead to better in silico prediction of soil mycobiome functions from Taiwan’s offshore islands
YF Lin*, WA Liu, YC Liu, HH Lee, YR Lin, PY Yu, EH Chang, MJ Lu, CY Chiu and IJ Tsai*

2023

Evolution and diversity of bioluminescent fungi
HM Ke, MR Lu, CC Chang, C Hsiao, JH Ou, Y Taenyama, CY Chen and IJ Tsai
Mycota 14

Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria
N Sahu, B Indic, J Wong-Bajracharya, Z Merényi, HM Ke, S Ahrendt, T Monk, S Kocsubé, E Drula, A Lipzen, B Bálint, B Henrissat, B Andreopoulos, FM Martin, CB Harder, D Rigling, KL Ford, GD Foster, J Pangilinan, A Papanicolaou, K Barry, K LaButti, M Virágh, M Koriabine, M Yan, R Riley, S Champramary, KL Plett, IV Grigoriev, IJ Tsai, J Slot, G Sipos, J Plett and LG Nagy (2023).
Nature Microbiology

Single-worm long-read sequencing reveals genome diversity in free-living nematodes
YC Lee, HM Ke, YC Liu, HH Lee, MC Wang, YC Tseng, T Kikuchi and IJ Tsai*
Nucleic Acid Research

Detecting intragenic trans-splicing events from non-co-linearly spliced junctions by hybrid sequencing
YC Chen, CY Chen, TW Chiang, MH Chan, M Hsiao, HM Ke, IJ Tsai and TJ Chuang.
Nucleic Acid Research
全基因體擴增技術定序無法培養的物種: 揭秘海洋線蟲的基因體多樣性

The Aphelenchoides genomes reveal substantial horizontal gene transfers in the last common ancestor of free-living and major plant-parasitic nematodes
CK Lai, YC Lee, HM Ke, MR Lu, WA Liu, HH Lee, YC Liu, T Yoshiga, T Kikuchi, PJ Chen* and IJ Tsai*.
Molecular Ecology Resources
揭示植物寄生線蟲水平基因轉移的演化史

Investigation of asymptomatic infection of Phellinus noxius in herbaceous plants CY Chen, ZC Wu, TY Lu, SS Yu, JN Tsai, YC Tsai, IJ Tsai and CL Chung
Phytopathology

The mitochondrial genome of Isognomon nucleus and mitogenomics of pteriomorphia (Bivalvia: Autobranchia)
N Dreyer, FMG Mattos, D Jain, CL Fong, MD Vivo, YHV Wen, YH Huang, JK Mwihaki, HH Lee, PC Tsai, YF Tsao, BKK Chan, IJ Tsai, R Machida, TY Wang and J Wang
Journal of Molluscan Studies**

2022

Investigation of asymptomatic infection of Phellinus noxius in herbaceous plants
CY Chen, ZC Wu, TY Liu, SS Yu, JN Tsai, YC Tsai, IJ Tsaiand CL Chung
Phytopathology

Translocation of fungicides and their efficacy in controlling Phellinus noxius, the cause of brown root rot disease
TZ Liao, YH Chen, JN Tsai, C Chao, TP Huang, CF Hong, ZC Wu, IJ Tsai, HH Lee, NB Klopfenstein, MS Kim, JE Stewart, N Atibalentja, FE Brooks, P Cannon, AM Farid, T Hattori, HS Kwan, YCR Lam, Y Ota, N Sahashi, RL Schlub, LS Shuey, AMC Tang and CL Chung
Plant Disease

Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization
DZ Hoh, HH Lee, N Wada, WA Liu, MR Lu, HM Ke, PF Sun, LH Hsu, WH Chung, SL Tang, YL Chen, CL Chung and IJ Tsai*
BMC Biology
中研院訊：跨動植物界的致病菌——茄鐮孢菌複合種染色體演化和其感染海龜蛋的模式

Genome assembly and evolutionary analysis of the Mandarin Duck, Aix galericulata
CS Ng†, CK Lai†, HM Ke, CF Chen, PC Tang, HC Cheng, WH Li* and IJ Tsai*
Genome Biology and Evolution

The teenage years of yeast population genomics — trace history, admixing and getting wilder
IJ Tsai
Current Opinion in Genetics & Development

Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum
FMG Mattos†, HH Lee†, YH Huang†, N Dreyer, D Jain, CL Fong, MD Vivo, YHV Wen, JK Mwihaki, HPC Tsai, YF Tsao, BKK Chan, R Machida, TY Wang, J Wang and IJ Tsai
Scientific reports

Possible stochastic sex determination in Bursaphelenchus nematodes
R Shinya, S Sun, M Dayi, IJ Tsai, A Miyama, AF Chen, K Hasegawa, I Antoshechkin, T Kikuchi and PW Sternberg
Nature Communications

Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages
TJ Lee, YC Liu, WA Liu, YF Lin, HH Lee, HM Ke, JP Huang, MJ Lu, CL Hsieh, KF Chung, G Liti and IJ Tsai
Genome Research
研之有物：熟悉的陌生人：做麵包、釀酒以外，臺灣森林無所不在的野生釀酒酵母菌

Yeasts from temperate forests
S Mozzachiodi, FY Bai, P Baldrian, G Bell, K Boundy-Mills, P Buzzini, N Čadež, FA Cubillos, S Dashko, R Dimitrov, KJ Fisher, B Gibson, D Gouliamova, D Greig, L Heistinger, CT Hittinger, M Jecmenica, V Koufopanou, CR Landry, T Mašínová, ES Naumova, D Opulente, JJ Peña, U Petrovič, IJ Tsai, B Turchetti, P Villarreal, A Yurkov, G Liti and P Boynton
Yeast

C. elegans BLMP-1 controls apical epidermal cell morphology by repressing expression of mannosyltransferase bus-8 and molting signal mlt-8
YZ Wu, HS Jiang, HFen Han, PH Li, MR Lu, IJ Tsai and YC Wu
Developmental Biology

Understanding and using fungal bioluminescence – recent progress and future perspectives
HM Ke and IJ Tsai
Current Opinion in Green and Sustainable Chemistry

2021

The brown root rot fungus Phellinus noxius affects microbial communities in different root-associated niches of Ficus trees
TY Liu, CH Chen, YL Yang, IJ Tsai, YN Ho, and CL Chung
Environmental Microbiology

The rectal mucosal but not fecal microbiota detects subclinical ulcerative colitis
YF Lin†, CM Sung†, HM Ke, WA Liu, HY Huang, MJ Lu, IJ Tsai* and SY Hsieh*
Gut Microbes

Biogeographic Changes in Forest Soil Microbial Communities of Offshore Islands—A Case Study of Remote Islands in Taiwan
EH Chang, IJ Tsai, SH Jien, GL Tian and CY Chiu
Forests

2020

Mycena genomes resolve the evolution of fungal bioluminescence
HM Ke*, HH Lee, CYI Lin, YC Liu, MR Lu, JWA Hsieh, CC Chang, PH Wu, MJ Lu, JY Li, G Shang, RJH Lu, LG Nagy, PY Chen, HW Kao and IJ Tsai*
PNAS

中研院：臺灣也有發光菇！中研院追溯基因演化史 找尋蕈類發光的意義
中央社：蕈類為什麼會發光 中研院用台灣菇解謎
蘋果日報：真是台灣之「光」！中研院用台灣菇解開「野菇發光」原理　登國際期刊

Chromosome-level genome assembly of the pinewood nematode Bursaphelenchus xylophilus strain Ka4C1
M Dayi, S Sun, Y Maeda, R Tanaka, A Yoshida, IJ Tsai and T Kikuchi
Microbiology Resource Announcements

Establishment of three human induced pluripotent stem cell lines from a type 1 diabetic family harboring sequence variants associated with autoimmunity
EP Chu†, CH Lin†, CHH Cho†, IF Cheng†, TC Kuo, RY Chen, CN Liao, JC Cheng, IJ Tsai, PC Wang, SJ Chang and CN Shen
Stem Cell Research

Comparative transcriptomics between free-living and parasitic nematode species reveals concerted correlation
MR Lu, CK Lai, BY Liao and IJ Tsai Genome Biology and Evolution

Nest microbiota and pathogen abundance impact hatching success in sea turtle conservation DZ Hoh, YF Lin, WA Liu, SNM Sidique and IJ Tsai
Fungal Ecology

Natural diversity in the predatory behavior facilitates the establishment of a new robust model strain for nematode-trapping fungi
CT Yang†, GV Ulzurrun†, HC Lin, CW Chang, SA Chen, CK Lai, IJ Tsai, FC Schroeder, JE Stajich and YP Hsueh
PNAS

Population genomics reveals genome plasticity in Paramecium bursaria YH Cheng, CFJ Liu, YH Yu, YT Jhou, IJ Tsai and JY Leu BMC Biology

2019

Soil is not a reservoir for Phellinus noxius
ZC Wu, YY Chang, QJ Lai, HA Lin, SS Tzean, RF Liou, IJ Tsai and CL Chung
Phytopathology

Evidence of extensive intraspecific noncoding reshuffling in a 169-kb mitochondrial genome of a basidiomycetous fungus Genome Biology and Evolution
HH Lee, HM Ke, CYI Lin, TJ Lee, CL Chung and IJ Tsai
Genome Biology and Evolution

Sequential changes in the host gut Microbiota during Infection with the intestinal parasitic nematode Strongyloides venezuelensis
T Afrin, K Murase, A Konosu, VL Hunt, M Bligh, Y Maeda, A Hino, H Maruyama, IJ Tsai and T Kikuchi
Frontier Cell. Infect. Microbiol

Predicting clinical outcomes of cirrhosis patients with hepatic encephalopathy from fecal microbiome
CM Sung†, YF Lin†, KF Chen†, HM Ke, CC Wu, HY Huang, YN Gong, WS Tsai, JF You, MJ Lu, HT Cheng, IJ Tsai* and SY Hsieh*
Cellular and Molecular Gastroenterology and Hepatology

Stage-specific transcriptome of Bursaphelenchus xylophilus reveals temporal regulation of effector genes and roles of the dauer-like stages in the lifecycle SE Tanaka, M Dayi, Y Maeda, IJ Tsai, R Tanaka, M Bligh, Y Takeuchi-Kaneko, K Fukuda, N Kanzaki and T Kikuchi Scientific Reports

Structure and Diversity of Soil Bacterial Communities in Offshore Islands
YT Lin, YF Lin, IJ Tsai, EH Chang, SHao Jien, YJu Lin & CY Chiu
Scientific Report

Blast fungal genomes show frequent chromosomal changes, gene gains and losses, and effector gene turnover
LBG Luciano, IJ Tsai, I Chuma, Y Tosa, YH Chen, JY Li, MY Li, MJ Lu, H Nakayashiki and WH Li
Molecular Biology Evolution

Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution
SM Chaw†, YC Liu, HY Wang, YW Wu, CI Lin, CS Wu, HM Ke, LY Chang, CY Hsu, HT Yang, E Sudianto, MH Hsu, KP Wu, NN Wang, J Leebens-Mack, and IJ Tsai†
Nature Plants
中研院：搶救國寶牛樟！ 牛樟全基因體定序重寫植物族譜
中央社：國寶牛樟基因體定序解碼 可望用於復育

Selected publications before 2019

Parasite genomics

Comparative genomics of the major parasitic worms
International Helminth Genomes Consortium (including IJ Tsai, TH Kuo, HM Ke and TJ Lee), A Coghlan, M Mitreva and M Berriman
Nature Genetics

Discovery, biology and genome of Caenorhabditis inopinata, a sibling of C. elegans
N Kanzaki†, IJ Tsai†, R Tanaka†, VL Hunt†, D Liu, K Tsuyama, Y Maeda, S Namai, R Kumagai, A Tracey, N Holroyd, SR Doyle, GC Woodruff, K Murase, H Kitazume, C Chai, A Akagi, O Panda, HM Ke, FC Schroeder, J Wang, M Berriman, PW Sternberg, A Sugimoto and T Kikuchi
Nature Communications

中研院：解開線蟲模式物種身世之謎！發現秀麗隱桿線蟲的近緣種
Author commentry: Caenorhabditis inopinata: the unexpected sibling species of C. elegans

The Genomic Basis of Parasitism in the Strongyloides Clade 1 of Nematodes
VL Hunt†, IJ Tsai†, A Coghlan†, AJ Reid†, N Holroyd, BJ Foth, A Tracey, JA Cotton, EJ Stanley, H Beasley, H Bennett, K Brooks, B Harsha, R Kajitani, A Kulkarni, D Harbecke, E Nagayasu, S Nichol, Y Ogura, MA Quail, N Randle, DM Ribeiro, A Sanchez-Flores, T Hayashi, T Itoh, DR Denver, W Grant, JD Stoltzfus, JB Lok, H Murayama, J Wastling, A Streit, T Kikuchi, M Viney and M Berriman
Nature Genetics
中時：台日英學者破解線蟲基因 研發疫苗有望
BBC：英日台專家聯手破解致命寄生蟲基因密碼

Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction
BJ Foth†, IJ Tsai†, AJ Reid†, AJ Bancroft†, S Nichol, A Tracey, N Holroyd, JA Cotton, EJ Stanley, M Zarowiecki, JZ Liu, T Huckvale, PJ Cooper, RK Grencis & M Berriman
Nature Genetics
BBC news Asia : 台灣與英國科學家聯手破解鞭蟲鑽孔基因

The genomes of four tapeworm species reveal adaptations to parasitism
IJ Tsai†, M Zarowiecki†, N Holroyd†, A Garciarrubio†, A Sanchez-Flores, KL Brooks, A Tracey, R J Bobes, G Fragoso, E Sciutto, M Aslett, H Beasley, X Cai, F Camicia, R Clark, M C, N De Silva, T A Day, P Deplazes, K Estrada, C Fernández, PWH Holland, J Hou, S Hu, T Huckvale, SS Hung, L Kamenetzky, JA Keane, F Kiss, U Koziol, O Lambert, K Liu, X Luo, Y Luo, N Macchiaroli, S Nichol, J Paps, Jn Parkinson, N Pouchkina-Stantcheva, N Riddiford, M Rosenzvit, G Salinas, JD Wasmuth, M Zamanian, Y Zheng, The Taenia solium Genome Consortium, J Cai, X Soberón, PD Olson, JP Laclette, K Brehm and M Berriman.
Nature
1.pansci: 基因體解析顯露絛蟲治療新策略
2.BBC news Asia : 抗癌藥可以用來抗擊絛蟲感染
3.BBC news: ‘Weakness mining’ for tapeworm drugs”
4.Reuters: Tapeworm genome points way to better drug treatments

A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni.
AV Protasio†, IJ Tsai†, A Babbage, S Nichol, M Hunt, ND Silva, TJC Anderson, RC Clark, C Davidson, GP Dillon, NE Holroyd, PT LoVerde, C Lloyd, J McQuillan, G Oliveira, TD Otto, SJ Parker-Manuel, MA Quail, RA Wilson, A Zerlotini, DW Dunne and M Berriman
PLoS Neglected Tropical Diseases PLoS Negl Trop Dis

Fungal genomics

Comparative and population genomics landscape of Phellinus noxius: a hypervariable fungus causing root rot in trees
CL Chung†, TJ Lee, M Akiba, HH Lee, TH Kuo, D Liu, HM Ke, T Yokoi, MB Roa, MJ Lu, YY Chang, PJ Ann, JN Tsai, CY Chen, SS Tzean, Y Ota, T Hattori, N Sahashi, RF Liou, T Kikuchi† and IJ Tsai†
Molecular Ecology
解密樹木褐根病 ─ 有害木層孔菌基因體發表

Population genomics of domestic and wild yeasts
G Liti, DM Carter, AM Moses, J Warringer, L Parts, SA James, RP Davey, IN Roberts, A Burt, V Koufopanou, IJ Tsai, CM Bergman, D Bensasson, MJT O’Kelly, A Oudenaarden, DBH Barton, E Bailes, AN Nguyen, M Jones, MA Quail, I Goodhead, S Sims, F Smith, A Blomberg, R Durbin & EJ Louis
Nature

Conservation of recombination hotspots in yeast
IJ Tsai, A Burt and V Koufopanou
PNAS

Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle
IJ Tsai, D Bensasson, A Burt and V Koufopanou
PNAS

Bioinformatics

Inferring synteny between genome assemblies: a systematic evaluation
D Liu, M Hunt and IJ Tsai
BMC Bioinformatics

Post-assembly genome- improvement from contigs to annotated genomes
MT Swain, IJ Tsai, SA Assefa, C Newbold, M Berriman and TD Otto
Nature Protocols

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
IJ Tsai, TD Otto and M Berriman.
Genome Biology