(1) Evolutionary developmental of flowers
(2) Plastid genomes in non-photosynthetic plants
(3) Phylogenetic systematics

       Our lab has been doing three lines of studies, first is on the evolutionary developmental biology of flowers, second is on the plastid genome evolution in non-photosynthetic plants; and third is on phylogenetic systematics. 

(1) Evolutionary developmental of flowers.
We are interested in transference of function in floral organs, and the putative mechanism behind this phenomenon. In particular, we are interested in the molecular developmental study of petaloid structure in plants. The rationale is based on the study in Arabidopsis that the ectopic expression of petal identity genes in Arabidopsis has shown to be sufficient turning sepals or leaves into petal-like structures. However, we only find weak expression of some, but not all, of the identified B-class genes in the showy bracts of dogwoods (Cornus florida) or calycophylls of Mussaenda pubescens, suggesting a different mechanism existed for controlling the petaloid structure in various plants. This work is still ongoing and several other approaches have been employed to elucidate the mechanism of petaloid formation. We are also interested in the evolution of floral organ identity genes among basal core-eudicots, including Trochodendrales, Santalales, Saxifragaceae (s.s.), and Ranunculales. These plants show vast variations in floral structure and are keys to elucidate the perianth evolution in eudicots. We are examining a putative duplication event of floral organ identity genes among these lineages, as well as the expression patterns of these genes. 

(2) Plastid genomes in non-photosynthetic plants.
We have selected several non-photosynthetic plants, either parasitic or saprophytic, to examine presence of plastid genome, including Balanophora, Mitrastema, Cheilotheca, and etc. We are also interested to know if they still harbor other photosystem related genes in their nuclear genome. 

(3) Phylogenetic systematics.
Currently we are working on the phylogenies of Chrysosplenium (Saxifragaceae), Balanophoraceae, and Millettieae (Fabaceae). We are also interested in studies of principles and methods of phylogenetic reconstruction.

Su, H.-J., J.-M. Hu, F. E. Anderson, J. Der, D. L. Nickrent*. 2015. Phylogenetic relationships of Santalales with insights into the origins of holoparasitic Balanophoraceae. Taxon 64(3): 491-506.

Tseng, Y. H. and J.-M. Hu*. 2015. Taxonomic revision of Elatostema J. R. Forst. & G. Forst. (Urticaceae) in Taiwan. Taiwania 60: 23-32.

Yang, Y.-T., D.-Y. Lee, Y. Wang, J.-M. Hu, W.-H. Li, J.-H. Leu, G.-D. Chang, H.-M. Ke, S.-T. Kand, S.-S. Lin, G.-H. Kou, and C.-F. Lo*. 2014. The genome and occlusion bodies of marine Penaeus monodon nudivirus (PmNV, also known as MBV and PemoNPV) suggest that it should be assigned to a new nudivirus genus that is distinct from the terrestrial nudiviruses. BMC Genomics 15:628.

Sun, P.-L., C.-A. Mu, C.-C. Fan, Y.-C. Fan, J.-M. Hu, and Y.-M. Ju*. 2014. Cat favus caused by Microsporum incurvatum comb. nov.: the clinical and histopathological features, and molecular phylogeny. Medical Mycology 52: 276-284.

Tseng, Y.-H. and J.-M. Hu*. 2014. A new hybrid from Taiwan, Elatostema xhybrida (Urticaceae), is the first confirmed natural hybrid for Urticaceae. Phytotaxa 161(1): 43-60.

Ku, C. and J.-M. Hu*. 2014. Phylogenetic and cophylogenetic analyses of the leaf-nodule symbiosis in Ardisia subgenus Crispardisia (Myrsinaceae): evidence from nuclear and chloroplast markers and bacterial rrn operons. International Journal of Plant Sciences 175(1): 92-109.

Shyu, S.-Y. and J.-M. Hu*. 2013. Comparison of six DNA extraction procedures and the application of plastid DNA isolation methods in non-photosynthetic plants. Taiwania 58(4): 268-274.

Ku, C., J.-M. Hu, and C.-H. Kuo*. 2013. Complete plastid genome sequence of the basal Asterid Ardisia polysticta Miq. and comparative analyses of Asterid plastid genomes. PLoS ONE 8(4): e62548.

Yang, W.-C., J.-M. Hu*, and L.-S. Chou*. 2013. Sequence analyses of MHC Class II DQB gene in bottlenose dolphins (Tursiops spp.) and the other delphinid species from the western Pacific. Taiwan Veterinary Journal 39(2): 100-109.

Su, H.-J. and J.-M. Hu*. 2012. Rate heterogeneity in six protein-coding genes from the holoparasite Balanophora (Balanophoraceae) and other Santalales taxa. Annals of Botany 110: 1137-1147.

Su, H.-J., J. Murata, and J.-M. Hu*. 2012. Morphology and phylogenetics of two holoparasitic plants, Balanophora japonica and Balanophora yakushimensis (Balanophoraceae), and their hosts in Taiwan and Japan. Journal of Plant Research 125: 317-326.

Pan, Z.-J., C.-C. Cheng, W.-C. Tsai, M.-C. Chung, W.-H. Chen, J.-M. Hu*, and H.-H. Chen*. 2011. The duplicated B-class MADS-box genes display dualistic characters in orchid floral organ identity and growth. Plant Cell Physiology 52: 1515-1531.

Wang, Y.-C. and J.-M. Hu*. 2011. Cryptic dioecy of Symplocos wikstroemiifolia Hayata (Symplocaceae) in Taiwan. Botanical Studies 52: 479-491.

Yang, W.-C., J.-M. Hu, and L.-S. Chou*. 2010. Phylogenetic analyses of MHC class II genes in bottlenose dolphins and their terrestrial relatives reveal pathogen-driven directional selection. Zoological Studies 49: 132-151.

Huang, J.-Y. and J.-M. Hu*. 2009. Revision of Rubus (Rosaceae) in Taiwan. Taiwania 54: 285-310.

Fu, H.-C., J.-M. Hu, T.-H. Hung, H.-J. Su, and H.-H. Yeh*. 2009. Unusual events involved in Banana bunchy top virus strain evolution. Phytopathology 99: 812-822.

Tseng, Y.-H., C.-F. Hsieh, and J.-M. Hu*. 2008. Incidences and ecological correlates of dioecious angiosperms in Taiwan and its outlying Orchid Island. Botanical Studies 49: 261-276.

Yang, W.-C., J.-M. Hu*, and L.-S. Chou*. 2008. Sequence variation of MHC Class II DQB gene in bottlenose dolphin (Tursiops truncatus) from Taiwanese waters. Taiwania 53: 42-50.

Chang, C.-S., Y.-H. Li, L.-T. Chen, W.-C. Chen, W.-P. Hsieh, J. Shin, W.-N. Jane, S.-J. Chou, G. Choi, J.-M. Hu, S. Somerville, S.-H. Wu*. 2008. LZF1, a HY5-regulated transcriptional factor, functions in Arabidopsis de-etiolation. Plant Journal 54: 205-219.

Yang, W.-C., L.-S. Chou, and J.-M. Hu*. 2007. Molecular characterization of major histocompatibility complex class II DQB and DRB genes in bottleneck dolphins (Tursiops truncatus and T. aduncus) from the Western Pacific. Zoological Studies 46: 664-679.

Wu, H.-C., H.-J. Su, and J.-M. Hu*. 2007. The identification of A-, B-, C-, and E-class MADS-box genes and implications for perianth evolution in the basal eudicot Trochodendron aralioides (Trochodendraceae). International Journal of Plant Sciences168: 775-799.

Hu, J.-M.*, H.-C. Fu, C.-H. Lin, H.-J. Su, and H.-H. Yeh. 2007. Reassortment and concerted evolution in banana bunchy top virus genome. Journal of Virology 81: 1746-1761.

Kramer, E. M.*, H.-J. Su, C.-C. Wu, and J.-M. Hu. 2006. A simplified explanation for the frameshift mutation that created a novel C-terminal motif in the APETALA3 gene lineage. BMC Evolutionary Biology 6: 30.

Chuang, S.-L. and Hu, J.-M.* 2004. The evolution of chloroplast matK genes, including identification of new homologues from Ophioglossum petiolatum and two lycophytes. Taiwania 49(4): 273-291.

Hu, J.-M.* and Chang S.-P. 2003. Two new members of the Callerya group (Fabaceae) based on phylogenetic analysis of rbcL sequences: Endosamara racemosa (Roxb.) Geesink and Callerya vasta (Kosterm.) Schot. Taiwania 48(2): 118-128.

Hu, J.-M.*, M. Lavin, M. F. Wojciechowski, and M. J. Sanderson. 2002. Phylogenetic analysis of nuclear ribosomal ITS/5.8S sequences in the tribe Millettieae (Fabaceae): Poecilanthe-Cyclolobium, the core Millettieae, and the Callerya group. Systematic Botany 27(4): 722-733.

Pennington, T., M. Lavin, H. Ireland, B. Klitgaard, J. Preston, and J.-M. Hu. 2001. Phylogenetic relationships of basal papilionoid legumes based on sequences of the chloroplast trnL intron.  Systematic Botany 26(3): 537-556.

Sanderson, M. J., M. F. Wojciechowski, J.-M. Hu, T. Sher Khan, and S. G. Brady. 2000.  Error, bias and long branch attraction in data for two chloroplast photosystem genes in seed plants. Molecular Biology and Evolution 17(5): 782-797.

Hu, J.-M.*, M. Lavin, M. Wojciechowski, and M. J. Sanderson. 2000. Phylogenetic systematics of the tribe Millettieae (Leguminosae) based on trnK/matK sequences, and its implications for the evolutionary patterns in Papilionoideae. American Journal of Botany 87(3): 418-430.

Wojciechowski, M., M. J. Sanderson, and J.-M. Hu. 1999. Evidence on the monophyly of Astragalus (Fabaceae) and its major subgroups based on nuclear ribosomal DNA ITS and chloroplast DNA trnL intron data. Systematic Botany 24(3): 409-437.

Lavin, M., E. Eshbaugh, J.-M. Hu, S. Mathews, and R. A. Sharrock. 1998. Monophyletic subgroups of the tribe Millettieae (Leguminosae) as revealed by phytochrome nucleotide sequence data. American Journal of Botany 85(3): 412-433.

Fu, J.-F., J.-M. Hu, Y.-S. Chang, and S.-T. Liu. 1998. Isolation and characterization of plasmid pSW200 from Erwinia stewartii.  Plasmid 40: 100-112.