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Chloroplast Genomes of Seven Coryloideae Species: Structures and Comparative Analysis

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Chloroplast Genomes of Seven Coryloideae Species: Structures and Comparative Analysis Genome Chloroplast genomes of seven Coryloideae species: structures and comparative analysis Journal: Genome Manuscript ID gen-2019-0153.R1 Manuscript Type: Article Date Submitted by the 22-Feb-2020 Author: Complete List of Authors: Hu, Guanglong; Beijing Academy of Forestry and Pomology Sciences; Beijing Academy of Agricultural and Forestry Sciences, National Forestry and Grassland Administration, Ministry of Agriculture and Rural Affairs/Chestnut Engineering Technology Research Center, Key LaboratoryDraft of Biology and Genetic Improvement of Horticultural Crops (North China) Cheng, Lili; Beijing Academy of Forestry and Pomology Sciences; Beijing Academy of Agricultural and Forestry Sciences, National Forestry and Grassland Administration, Ministry of Agriculture and Rural Affairs/Chestnut Engineering Technology Research Center, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) Huang, Wugang; Beijing Academy of Forestry and Pomology Sciences; Beijing Academy of Agricultural and Forestry Sciences, National Forestry and Grassland Administration, Ministry of Agriculture and Rural Affairs/Chestnut Engineering Technology Research Center, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) Cao, Qingchang; Beijing Academy of Forestry and Pomology Sciences; Beijing Academy of Agricultural and Forestry Sciences, National Forestry and Grassland Administration, Ministry of Agriculture and Rural Affairs/Chestnut Engineering Technology Research Center, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) Zhou, Lei; Hubei Academy of Agricultural Sciences, Food Crops Institute, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement Jia, Wenshen; Beijing Academy of Agriculture and Forestry Science, Department of Beijing Research Center for Agricultural Standards and Testing Lan, Yanping; Beijing Academy of Forestry and Pomology Sciences; Beijing Academy of Agricultural and Forestry Sciences, National Forestry and Grassland Administration, Ministry of Agriculture and Rural Affairs/Chestnut Engineering Technology Research Center, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) Corylus, Coryloideae, illumina sequencing, phylogenetic relationship, Keyword: Chloroplast genome (plastome) https://mc06.manuscriptcentral.com/genome-pubs Page 1 of 40 Genome Is the invited manuscript for consideration in a Special Not applicable (regular submission) Issue? : Draft https://mc06.manuscriptcentral.com/genome-pubs Genome Page 2 of 40 1 Title 2 Chloroplast genomes of seven Coryloideae （ Betulaceae ） species: structures and 3 comparative analysis 4 Authors and affiliations 5 ‘ 6 Guanglong Hua,b,†,*, Lili Chenga,b,†, Wugang Huanga,b, Qingchang Caoa,b, Lei Zhouc, 7 Wenshen Jiad, Yanping Lana,b,* 8 a Beijing Academy of Forestry and Pomology Sciences, Beijing 100093, China Draft 9 b Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North 10 China), Ministry of Agriculture and Rural Affairs/Chestnut Engineering Technology 11 Research Center, National Forestry and Grassland Administration, Beijing Academy of 12 Agricultural and Forestry Sciences, Beijing 100093, China 13 c Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food 14 Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, 15 China 16 d Department of Beijing Research Center for Agricultural Standards and Testing, 17 Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China 18 † The authors contributed equally to this work. 19 * Corresponding authors: Guanglong Hu (email: [email protected]) and Yanping Lan 20 ([email protected]). 1 https://mc06.manuscriptcentral.com/genome-pubs Page 3 of 40 Genome 21 Abstract 22 Coryloideae is a subfamily in the family Betulaceae consisting of four extant genera 23 Carpinus, Corylus, Ostrya , and Ostryopsis. We sequenced the plastomes of six 24 Corylus and one Ostryopsis species for comparative and phylogenetic analyses. The 25 plastomes are 159–160 kb long and possess the typical quadripartite cp architecture. 26 The plastomes show moderate divergence and conserved arrangement. We pointed five 27 mutational hotspots: trnG-atpA, trnF-ndhJ, accD-psaI, ndhF-ccsA, and ycf1, by 28 comparing the Coryloideae plastomes. We brought the most complete phylogenomic 29 tree for the family Betulaceae Draftusing 68 plastomes. Our cp genomic sequence 30 phylogenetic analyses placed Carpinus, Ostrya and Ostryopsis in a clade together and 31 left Corylus in a separate clade. Within the genus Corylus, these analyses indicate the 32 existence of five subclades reflecting the phylogeographical relationships among the 33 species. The data offer significant genetic information for the identification of 34 Coryloideae species, taxonomic and phylogenetic studies, and molecular breeding. 35 Key words 36 Corylus, Coryloideae, chloroplast genome, illumina sequencing, phylogenetic 37 relationship. 2 https://mc06.manuscriptcentral.com/genome-pubs Genome Page 4 of 40 38 Introduction 39 The Betulaceae Gray.(birch) family has six genera containing 120–150 species 40 (Abbe, 1974; Chen, 1994; Furlow, 1990). A majority of the species in the family are 41 primarily concentrated in the northern hemisphere. The six Betulaceae genera are 42 divided into two main tribes: Betuleae (Alnus Mill.and Betula L. ), and Coryleae 43 (Carpinus L., Corylus L., Ostrya Scop. , and Ostryopsis Decne.) ( Prantl and Engler, 44 1887; Winkler, 1904;Crane, 1989). Some authors suggest that the two tribes should be 45 elevated to the subfamilies Betuloideae and Coryloideae ( Rendle, 1925; Jury, 1978; 46 Furlow, 1990; Chen et al., 1999). DraftMoreover, the position of Ostryopsis in Coryleae is 47 controversial ( Kuprianova, 1963; Abbe, 1974; Furlow, 1990; Chen, 1994 ). Several 48 opinions concerning the genetic relationships among the genera of Coryleae have been 49 presented in the literature, using morphological characters, as well as rbcL gene and 50 ribosomal internal transcribed spacer (ITS) sequences (Abbe, 1974; Furlow, 1990; 51 Bousquet et al., 1992; Chen, 1994) 52 Ostryopsis davidiana Decne., one of two species in the genus Ostryopsis, is natively 53 distributed across vast northern areas of China (Raven, 1975; Li and Skvortsov, 1999; 54 Tian et al., 2009). The genus Corylus has 14 to 18 species concentrated in the northern 55 hemisphere’s temperature areas (Chen et al., 1999). Seven of those species grow in 56 China and comprise three tree species (C. chinensis Franch, C. fargesii C.K. Schneider, 57 and C. ferox Wall) and four shrub species (C. heterophylla Fisch, C. yunnanensis A. 58 Camus, C. mandshurica Maxim, and C. wangii Hu) (Liang and Zhang, 1988). However, 3 https://mc06.manuscriptcentral.com/genome-pubs Page 5 of 40 Genome 59 there is disagreement about whether C. yunnanensis and C. wangii should be 60 recognized as distinct species (Whitcher and Wen, 2001; Yoo and Wen, 2007). In 61 addition, most species of Corylus can hybridize with each other to achieve the cpDNA 62 introgression and transfer interspecificly (Erdogan and Mehlenbacher,2000b), therefor 63 the phylogeny and species definition of Corylus are still not completed. 64 The majority of plant plastomes typically possess a quadripartite architecture: two 65 inverted repeats (IRa and IRb), a small single copy region (SSC), and a large single 66 copy region (LSC). The plastome is usually circular DNA, of which 115–165 kb is 67 highly conserved. It has a conserved gene order and gene content ( Dong et al., 68 2013b;Wambugu et al., 2015; AsafDraft et al., 2016). Comparatively, the substitution rate 69 of a plant nuclear genome is higher than that of a cp genome (Duchene and Bromham, 70 2013; Smith, 2015). Furthermore, the angiosperm plastome has a stable structure, and 71 offer genetic markers sufficient for genome-wide evolutionary investigation at various 72 taxonomic levels ( Wu et al., 2010; Dong et al., 2012; Zhang et al., 2017；Givnish et 73 al., 2018;). Even though the plant plastome is evolutionarily conserved, specific 74 lineages and genes exhibit accelerated evolution rates ( Wu et al., 2010; Gaut et al., 75 2011; Dong et al., 2012, 2013b; Duchene and Bromham, 2013; Smith, 2015; Wambugu 76 et al., 2015;Asaf et al., 2016; Zhang et al., 2017). For instance, ycf1, matK, and rbcL 77 are all used, serving as DNA markers for barcoding plants ( Hollingsworth et al., 2011; 78 Dong et al., 2015). Due to such features, the plastome is assumed to serve as a good 4 https://mc06.manuscriptcentral.com/genome-pubs Genome Page 6 of 40 79 model for the investigation of lineage-specific molecular evolution (Sanitá Lima et al., 80 2016). 81 The plastomes of one Ostryopsis species and six Corylus species were sequenced in 82 this study via a next-generation sequencing platform. We gained valuable plastome 83 information including the length and content of highly variable regions, indels, 84 microsatellites, and single nucleotide polymorphisms (SNPs) in this subfamily by 85 comparing plastomes. Also, we assessed the phylogenetic relationships within the 86 Betulaceae genera and among the seven Coryloideae species. 87 Materials and methods Draft 88 Materials and DNA extraction 89 Fresh leaves of five Corylus species and O. davidiana were collected in China in 90 regions of natural distribution (Table 1). Fresh leaves of C. avellana were obtained from 91 the Germplasm Resource Nursery, Beijing Academy of Forestry and Pomology
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