De novo transcriptome analysis of Medicago falcata reveals novel insights about the mechanisms underlying abiotic stress-responsive pathway.
BACKGROUND
The entire world is facing a deteriorating environment. Understanding the mechanisms underlying plant responses to external abiotic stresses is important for breeding stress-tolerant crops and herbages. Phytohormones play critical regulatory roles in plants in the response to external and internal cues to regulate growth and development. Medicago falcata is one of the stress-tolerant candidate leguminous species and is able to fix atmospheric nitrogen. This ability allows leguminous plants to grow in nitrogen deficient soils.


METHODS
We performed Illumina sequencing of cDNA prepared from abiotic stress treated M. falcata. Sequencedreads were assembled to provide a transcriptome resource. Transcripts were annotated using BLASTsearches against the NCBI non-redundant database and gene ontology definitions were assigned. Acomparison among the three abiotic stress treated samples was carried out. The expression of transcriptswas confirmed with qRT-PCR.


RESULTS
We present an abiotic stress-responsive M. falcata transcriptome using next-generation sequencing data from samples grown under standard, dehydration, high salinity, and cold conditions. We combined reads from all samples and de novo assembled 98,515 transcripts to build the M. falcata gene index. A comprehensive analysis of the transcriptome revealed abiotic stress-responsive mechanisms underlying the metabolism and core signalling components of major phytohormones. We identified nod factor signalling pathways during early symbiotic nodulation that are modified by abiotic stresses. Additionally, a global comparison of homology between the M. falcata and M. truncatula transcriptomes, along with five other leguminous species, revealed a high level of global sequence conservation within the family.


CONCLUSIONS
M. falcata is shown to be a model candidate for studying abiotic stress-responsive mechanisms in legumes. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to abiotic stresses. Our data provides many gene candidates that might be used for herbage and crop breeding. Additionally, FalcataBase ( http://bioinformatics.cau.edu.cn/falcata/ ) was built for storing these data.
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. miaozhenyan@163.com.|Present address: Department of Agronomy, Purdue University, West Lafayette, IN, USA. miaozhenyan@163.com.
Zhenyan
Z
Miao
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China. xuw@big.ac.cn.
Wei
W
Xu
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. lidaof@gmail.com.|Present address: Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA. lidaof@gmail.com.
Daofeng
D
Li
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. huxiaona.109@163.com.
Xiaona
X
Hu
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. liujiaxing1986@126.com.
Jiaxing
J
Liu
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. zrx1230@163.com.
Rongxue
R
Zhang
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. dradon.tong@163.com.
Zongyong
Z
Tong
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. dongjl@cau.edu.cn.
Jiangli
J
Dong
State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. zhensu@cau.edu.cn.
Zhen
Z
Su
State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. lwzhanghz@163.com.
Liwei
L
Zhang
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China. sunm@big.ac.cn.
Min
M
Sun
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China. wjli@big.ac.cn.
Wenjie
W
Li
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China. duzhl@big.ac.cn.
Zhenglin
Z
Du
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China. husn@big.ac.cn.
Songnian
S
Hu
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China. wangt@cau.edu.cn.
Tao
T
Wang
D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D029902:Medicago / Q000235:genetics / Q000502:physiology; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D010940:Plant Proteins / Q000096:biosynthesis; D018517:Plant Roots / Q000235:genetics; D012965:Sodium Chloride / Q000737:chemistry; D013312:Stress, Physiological / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
D010940:Plant Proteins; D012965:Sodium Chloride