Assembly and comparative analyses of the mitochondrial genome of Castanospermum australe (Papilionoideae, Leguminosae)
Rong Zhang A B , Jian-Jun Jin A , Michael J. Moore C and Ting-Shuang Yi
A D
+ Author Affiliations
- Author Affiliations
A Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming, 650201, PR China.
B University of Chinese Academy of Sciences, Yuquan Road, Beijing, 100049, PR China.
C Department of Biology, Oberlin College, College Street, Oberlin, OH 44074, USA.
D Corresponding author. Email: tingshuangyi@mail.kib.ac.cn
Australian Systematic Botany 32(6) 484-494 https://doi.org/10.1071/SB19014
Submitted: 11 February 2019 Accepted: 5 April 2019 Published: 1 October 2019
Journal Compilation © CSIRO 2019 Open Access CC BY-NC-ND
Abstract
Plant mitochondrial genomes are often difficult to assemble because of frequent recombination mediated by repeats. Only a few mitochondrial genomes have been characterised in subfamily Papilionoideae of Leguminosae. Here, we report the complete mitochondrial genome of Castanospermum australe A.Cunn. & C.Fraser, an important medicinal and ornamental species in the Aldinoid clade of Papilionoideae. By mapping paired-end reads, seven hypothetical subgenomic conformations were rejected and two hypothetical complete isometric mitochondrial genome conformations that differed by a 64-kb inversion were strongly supported. Quantitative assessment of repeat-spanning read pairs showed a major conformation (MC1) and a minor conformation (MC2). The complete mitochondrial genome of C. australe was, thus, generated as 542 079 bp in length, with a high depth of coverage (~389.7×). Annotation of this mitochondrial genome yielded 58 genes encoding 37 proteins, 18 tRNAs and three rRNAs, as well as 17 introns and three medium-sized repeats (133, 119 and 114 bp). Comparison of 10 mitochondrial genomes from Papilionoideae demonstrated significant variation in genome size, structure, gene content and RNA editing sites. In addition, mitochondrial genes were shown to be potentially useful in resolving the deep relationships of Papilionoideae.
Additional keywords: genome skimming, legume, mitochondrion, Moreton Bay chestnut, phylogeny, read-pair mapping.
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