title: Protein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus.
abstract: Predicting protein domains is essential for understanding a protein's function at the molecular level. However, up till now, there has been no direct and straightforward method for predicting protein domains in species without a reference genome sequence. In this study, we developed a functionality with a set of programs that can predict protein domains directly from genomic sequence data without a reference genome. Using whole genome sequence data, the programming functionality mainly comprised DNA assembly in combination with next-generation sequencing (NGS) assembly methods and traditional methods, peptide prediction and protein domain prediction. The proposed new functionality avoids problems associated with de novo assembly due to micro reads and small single repeats. Furthermore, we applied our functionality for the prediction of leucine rich repeat (LRR) domains in four species of Ficus with no reference genome, based on NGS genomic data. We found that the LRRNT_2 and LRR_8 domains are related to plant transpiration efficiency, as indicated by the stomata index, in the four species of Ficus. The programming functionality established in this study provides new insights for protein domain prediction, which is particularly timely in the current age of NGS data expansion.
authors.affiliation: Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan Province, China.
authors.forename: Tiange
authors.initials: T
authors.lastname: Lang
authors.affiliation: College of Forestry, Beijing Forestry University, Beijing, China; School of Life Science, Tsinghua University, Beijing, China.
authors.forename: Kangquan
authors.initials: K
authors.lastname: Yin
authors.affiliation: Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan Province, China.
authors.forename: Jinyu
authors.initials: J
authors.lastname: Liu
authors.affiliation: Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan Province, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, and College of Forestry, Guangxi University, Nanning, Guangxi, China.
authors.forename: Kunfang
authors.initials: K
authors.lastname: Cao
authors.affiliation: Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan Province, China; Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America.
authors.forename: Charles H
authors.initials: CH
authors.lastname: Cannon
authors.affiliation: College of Forestry, Beijing Forestry University, Beijing, China.
authors.forename: Fang K
authors.initials: FK
authors.lastname: Du
mesh_terms: D000595:Amino Acid Sequence; D030681:Ficus / Q000737:chemistry / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D007930:Leucine / Q000737:chemistry / Q000378:metabolism*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D054046:Plant Stomata / Q000502:physiology; D018526:Plant Transpiration / Q000502:physiology; D017434:Protein Structure, Tertiary; D020449:Repetitive Sequences, Amino Acid
chemical_list: D010940:Plant Proteins; D007930:Leucine