The complete plastid genome of the endangered species midget crabapple ( Malus micromalus )

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TECHNICAL NOTE

The complete plastid genome of the endangered species midget crabapple (Malus micromalus) Yiheng Hu1 · Zhenhua Ma2 · Meng Dang1 · Xiaojia Feng1 · Yiwei Sun1 · Xiaoying Yuan1 · Xianheng Ouyang1 · Keith E. Woeste3 · Peng Zhao1 

Received: 6 August 2017 / Accepted: 31 August 2017 © Springer Science+Business Media B.V. 2017

Abstract  The midget crabapple (Malus micromalus) is endemic to Shaanxi and Shanxi Provinces of China. Like many other members of the Rosaceae, it is an important contributor to food production and nutrition. We determined the complete chloroplast genome sequences for M. micromalus using IIumina sequencing. The M. micromalus chloroplast has a total length of 159,834 bp; it consists of a large single copy (LSC) region of 87,950 bp, an inverted region A (IRa) of 26,354 bp, a short single copy (SSC) region of 19,176 bp, and an inverted region B (IRb) of 26,354 bp. The genome encodes 129 annotated genes, including 84 protein-coding genes and 45 tRNA. A phylogenomic analysis revealed that M. micromalus clustered with M. prunifolia within Malus.

Malus micromalus is a rare, endemic small tree. It is sporadically distributed in northern China in certain hilly,

mid-elevation areas of Shaanxi and Shanxi provinces. The fruit of M. micromalus is rich in vitamins and highly nutritious (Fang et al. 2017). The plant itself is highly resistant to drought (Vinatzer et al. 2004). M. micromalus has been extensively exploited for human-use, dramatically shrinking its natural populations. This species is considered on the brink of extinction and needs urgent conservation. Plastid genomes have been used extensively to understand plant genetic diversity and evolution and for conservation assessment. We assembled the complete chloroplast genome sequence of M. micromalus using the high-throughput Illumina paired-end sequencing data. The annotated plastid genome has been deposited into GenBank with the accession number: MF062434. Total genomic DNA was extracted from a single individual M. micromalus growing in Fugu County, Shaanxi, China (E110.85, N39.44). After trimming the sequences, high-quality PE reads were aligned to the M. prunifolia plastid genome (Genebank accession number: KU851961; Bao et  al. 2016) using bowtie2 v2.2.6 (Langmead and

* Peng Zhao [email protected]

Xianheng Ouyang [email protected]

Yiheng Hu [email protected]

Keith E. Woeste [email protected]

Zhenhua Ma [email protected]

1



Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Taibaibei Road 229, Xi’an 710069, Shaanxi, China

Xiaojia Feng [email protected]

2



Northwest Forestry Exploring Institute of China State Forestry Administration, Xi’an 710048, Shaanxi, China

Yiwei Sun [email protected]

3



USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, IN 47907, USA

Keywords  M. micromalus ·