Evidence map›Paper›PMID 38236432›Full record

ArticleFunctional & integrative genomics2024

Complete chloroplast genome of the Malus baccata var. gracilis provides insights into the evolution and phylogeny of Malus species.

Xin Qin, Qiang Hao, Xun Wang, Yangbo Liu, Chen Yang, Mengyi Sui, Yawen Zhang, Yanli Hu, Xuesen Chen, Zhiquan Mao and 2 more

Abstract read
PubMed Publisher
In one paragraph

Article in Functional & integrative genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors.

Xin Qin *College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China.
Qiang Hao *China National Botanical Garden (North Garden), Beijing, China.
Xun WangCollege of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China.
Yangbo LiuCollege of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China.
Chen YangCollege of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China.
Mengyi SuiCollege of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China.
Yawen ZhangCollege of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China.
Yanli HuCollege of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China.
Xuesen ChenCollege of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China.
Zhiquan MaoCollege of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China.
Yunfei MaoCollege of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China. myfmyf@sdau.edu.cn.
Xiang ShenCollege of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China. shenx@sdau.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Malus baccata (L.) var. gracilis (Rehd.) has high ornamental value and breeding significance, and comparative chloroplast genome analysis was applied to facilitate genetic breeding for desired traits and resistance and provide insight into the phylogeny of this genus. Using data from whole-genome sequencing, a tetrameric chloroplast genome with a length of 159,992 bp and a total GC content of 36.56% was constructed. The M. baccata var. gracilis chloroplast genome consists of a large single-copy sequence (88,100 bp), a short single-copy region (19,186 bp), and two inverted repeat regions, IRa (26,353 bp) and IRb (26,353 bp). This chloroplast genome contains 112 annotated genes, including 79 protein-coding genes (nine multicopy), 29 tRNA genes (eight multicopy), and four rRNA genes (all multicopy). Calculating the relative synonymous codon usage revealed a total of 32 high-frequency codons, and the codons exhibited a biased usage pattern towards A/U as the ending nucleotide. Interspecific sequence comparison and boundary analysis revealed significant sequence variation in the vast single-copy region, as well as generally similar expansion and contraction of the SSC and IR regions for 10 analyzed Malus species. M. baccata var. gracilis and Malus hupehensis were grouped together into one branch based on phylogenetic analysis of chloroplast genome sequences. The chloroplast genome of Malus species provides an important foundation for species identification, genetic diversity analysis, and Malus chloroplast genetic engineering. Additionally, the results can facilitate the use of pendant traits to improve apple tree shape.

Indexed as

Genome, ChloroplastMalusCodonPhylogenyPlant BreedingCodonBioinformaticsChloroplast genomeComparative genomics analysisMalus baccata var. gracilisPhylogeny

Identifiers

PMID38236432

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.