The Whole Genome Assembly and Comparative Genomic Research of Thellungiella parvula (Extremophile Crucifer) Mitochondrion

Abstract

The complete nucleotide sequences of the mitochondrial (mt) genome of an extremophile species Thellungiella parvula (T. parvula) have been determined with the lengths of 255,773 bp. T. parvula mt genome is a circular sequence and contains 32 protein-coding genes, 19 tRNA genes, and three ribosomal RNA genes with a 11.5% coding sequence. The base composition of 27.5% A, 27.5% T, 22.7% C, and 22.3% G in descending order shows a slight bias of 55% AT. Fifty-three repeats were identified in the mitochondrial genome of T. parvula, including 24 direct repeats, 28 tandem repeats (TRs), and one palindromic repeat. Furthermore, a total of 199 perfect microsatellites have been mined with a high A/T content (83.1%) through simple sequence repeat (SSR) analysis and they were distributed unevenly within this mitochondrial genome. We also analyzed other plant mitochondrial genomes' evolution in general, providing clues for the understanding of the evolution of organelles genomes in plants. Comparing with other Brassicaceae species, T. parvula is related to Arabidopsis thaliana whose characters of low temperature resistance have been well documented. This study will provide important genetic tools for other Brassicaceae species research and improve yields of economically important plants.

Figure 1

Circular gene map of the Thellungiella parvula mitochondrial genome. The T. parvula mitogenome consists of 54 genes, including 3 ribosomal RNA (rRNA) genes (5S rRNA, 26S rRNA, and rrnS), 19 transfer RNA (tRNA) genes, and 32 protein-coding genes.

Figure 2

The GBrowse of the Thellungiella parvula mitogenome, showing the detailed location of mitogenome, GC content, CDs, tRNA, and other useful information.

Figure 3

Frequency distribution of repeat lengths in the mitochondrial genome of Thellungiella parvula.

Figure 4

A phylogenetic context based on amino acid sequences of the fifteen protein-encoding genes (atp1, atp9, ccmB, cob, cox1, cox3, nad1, nad3, nad4, nad4L, nad6, nad7, nad9, rps3, and rps4) of twenty-one species (Brassica napus, Brassica rapa subsp. campestris, Brassica juncea, Raphanus sativus, Brassica carinata, Thellungiella parvula, Arabidopsis thaliana, Carica papaya, Vigna radiata, Citrullus lanatus, Cucumis sativus, Cucurbita pepo, Nicotiana tabacum, Silene latifolia, Beta vulgaris subsp. vulgaris, Beta vulgaris subsp. maritima, Oryza sativa Indica, Sorghum bicolor, Tripsacum dactyloides, Zea perennis, and Cycas taitungensis). These conserved genes were aligned with ClustalW and the phylogenetic tree was constructed using the Neighbor-Joining method in MEGA 6.

Figure 5

Maximum likelihood tree based on fifteen protein-encoding genes (atp1, atp9, ccmB, cob, cox1, cox3, nad1, nad3, nad4, nad4L, nad6, nad7, nad9, rps3, and rps4) of twenty-one species (Brassica napus, Brassica rapa subsp. campestris, Brassica juncea, Raphanus sativus, Brassica carinata, Thellungiella parvula, Arabidopsis thaliana, Carica papaya, Vigna radiata, Citrullus lanatus, Cucumis sativus, Cucurbita pepo, Nicotiana tabacum, Silene latifolia, Beta vulgaris subsp. vulgaris, Beta vulgaris subsp. maritima, Oryza sativa Indica, Sorghum bicolor, Tripsacum dactyloides, Zea perennis, and Cycas taitungensis). Numbers on each node are bootstrap support values. Cycas taitungensis is set as an out-group.