Ecological genomics of fungi and nematodes

真菌和線蟲生態基因體學研究

Publications 研究著作

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*
Biorxiv

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

Assessing the rectal mucosal microbiota improves mild ulcerative colitis detection sensitivity and evaluation
YF Lin†, CM Sung†, HM Ke, WA Liu, HY Huang, MJ Lu, IJ Tsai* and SY Hsieh*
Gut Microbes (in press)

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, HM Ke, 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

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