Characterization and Comparative Analysis of the Complete Chloroplast Genome of the Critically Endangered Species Streptocarpus Teitensis (Gesneriaceae)
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Hindawi BioMed Research International Volume 2018, Article ID 1507847, 11 pages https://doi.org/10.1155/2018/1507847 Research Article Characterization and Comparative Analysis of the Complete Chloroplast Genome of the Critically Endangered Species Streptocarpus teitensis (Gesneriaceae) Cornelius M. Kyalo ,1,2,3 Andrew W. Gichira,1,2,3 Zhi-Zhong Li,1,2,3 Josphat K. Saina,1,2,3 Itambo Malombe,4 Guang-Wan Hu ,1,3 and Qing-Feng Wang 1,3 1 Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China 2University of Chinese Academy of Sciences, Beijing 100049, China 3Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China 4East African Herbarium, National Museums of Kenya, P.O. Box 45166-00100, Nairobi, Kenya Correspondence should be addressed to Guang-Wan Hu; [email protected] and Qing-Feng Wang; [email protected] Received 18 October 2017; Revised 27 December 2017; Accepted 28 January 2018; Published 25 March 2018 Academic Editor: Stanley Brul Copyright © 2018 Cornelius M. Kyalo et al. Tis is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Streptocarpus teitensis (Gesneriaceae) is an endemic species listed as critically endangered in the International Union for Conservation of Nature (IUCN) red list of threatened species. However, the sequence and genome information of this species remains to be limited. In this article, we present the complete chloroplast genome structure of Streptocarpus teitensis and its evolution inferred through comparative studies with other related species. S. teitensis displayed a chloroplast genome size of 153,207 bp, sheltering a pair of inverted repeats (IR) of 25,402 bp each split by small and large single-copy (SSC and LSC) regions of 18,300 and 84,103 bp, respectively. Te chloroplast genome was observed to contain 116 unique genes, of which 80 are protein- coding, 32 are transfer RNAs, and four are ribosomal RNAs. In addition, a total of 196 SSR markers were detected in the chloroplast genome of Streptocarpus teitensis with mononucleotides (57.1%) being the majority, followed by trinucleotides (33.2%) and dinucleotides and tetranucleotides (both 4.1%), and pentanucleotides being the least (1.5%). Genome alignment indicated that this genome was comparable to other sequenced members of order Lamiales. Te phylogenetic analysis suggested that Streptocarpus teitensis is closely related to Lysionotus pauciforus and Dorcoceras hygrometricum. 1. Introduction Streptocarpus teitensis [6], previously known as Saint- paulia teitensis, is an endemic of Taita hills, Kenya, the Streptocarpus Lindley (Cape primroses) are herbaceous plant northernmost stretch of the Eastern arc mountain forests. Te species of the family Gesneriaceae and exhibit either annual species has experienced a drastic reduction in the distribution or perennial lifeforms. Te genus hosts approximately 176 rangeoverthepast,anditwasrecordedtoberestrictedtoa 2 species [1], distributed in Madagascar, Comoros islands, and single site (<2.5 km ) in the wild, Mbololo Hill [7], although some regions of Africa [2, 3], with the regions sharing no more than half of the range has deteriorated of late (personal single species [4]. Te genus, like most members of the observation, 2017). Tis restriction in distribution coupled family Gesneriaceae, hosts some species of great horticultural with other threats facing this species has led to its criti- importance such as Streptocarpus ionanthus which contribute cally endangered conservation status under the IUCN red a large percentage to the world’s fower industry [5]. list (http://www.iucnredlist.org/). Additionally, none of the 2 BioMed Research International species in this genus has been sequenced of its complete addition, the raw data was recognized through BLAST chloroplast genome. It is therefore essential to obtain the (https://blast.ncbi.nlm.nih.gov/) search against Lysionotus complete chloroplast genome sequence as a step towards gen- pauciforus (GenBank Number: KX752081) sequences since erating genomic resources that can aid future phylogenomic it showed the highest similarity. Tis produced sequence studies within this family. contigs which were organized and plotted against the already Techloroplastiscrucialforplantcellprocessessuchas published plastid sequences of Lysionotus pauciforus also photosynthesis [8–10] and physiological and development via BLAST (https://blast.ncbi.nlm.nih.gov/) with default set- processes such as leaf and root development [11–13]. Tis tings, in order to acquire the chloroplast genome reads. organelle owns a single circular DNA, which in angiosperms Tese reads were then assembled into contigs in Velvet 1.2.10 is four-structured made of two duplicates of inverted repeat [23].Analignmentoftheresultingcontigswithclosest (IR) regions, one large single-copy (LSC) region, and one chloroplast genomes of Lysionotus pauciforus and Haberlea small single-copy (SSC) region [14]. Almost all chloroplast rhodopensis (GenBank Number: KX657870) was done via (cp) genomes studied show a relatively limited size range BLAST (https://blast.ncbi.nlm.nih.gov/). occurring between 120 and 160 kilobase pairs [10, 14–16] and comprise 110–130 genes, of which four are ribosomal RNA 2.2. Genome Annotation. Te assembled cp genome was genes, ∼80 are protein-coding, and ∼30 are transfer RNAs annotated using the online program Dual Organellar [17]. GenoMe Annotator (DOGMA) [17], combined with manual Complete sequenced chloroplast genomes have numeri- alterations for the doubtful start and stop codons based on cally improved of late owing to the technical developments comparison with homologous genes from other sequenced in DNA sequencing [11, 18] such as the Next-Generation chloroplast genomes. Te annotation of the tRNA genes was Sequencing [19]. Te availability of chloroplast genomes verifed using tRNAscan-SE [24]. Te circular cp genome enables researchers to understand the evolution of the map was constructed by the use of online OGDRAW genomes, the structural organization, genes present, gene program [25]. Finally, the annotated genome sequences were order, and the nucleotide alignment [18]. It has also made submitted to the NCBI GenBank under Accession Number noteworthy contributions to phylogenetic studies of a signif- MF596485. icant number of plant families and determined their evolu- tionary links [11]. Tis has been made possible by the fact that 2.3. Genome Comparison and Phylogenetic Analysis. Te chloroplast genome has a simple and stable genetic structure genome features such as GC contents and size of S. teit- [20]. Over 1000 cp genomes are already completely sequenced ensis cp genome were compared with the available three and explained (https://blast.ncbi.nlm.nih.gov/) since 1986 chloroplast genomes in Gesneriaceae (Table 5) and 11 other when the frst chloroplast genome was sequenced in Tobacco species representing nine diferent families within the order [10]. However, since there are only three sequenced members Lamiales (Table 6), to check for similarities and variations. of the family Gesneriaceae, identifying the unique features Furthermore, all four species of Gesneriaceae (Lysionotus of the family’s chloroplast genome can lead to deceptive pauciforus, Haberlea rhodopensis, Dorcoceras hygrometricum estimates of species relations [21]. Tus, complete chloroplast [1] (previously known as Boea hygrometrica as in [26]), genomes from additional members of the family are essen- and Streptocarpus teitensis)wereusedtodoacomparative tial for comparative analysis to show structural variations study on the expansion and contraction of the IR regions. among the genomes. Te aims of this study were to present Tis was achieved through analysis of the four junctions, the frst whole chloroplast genome sequence of the genus a characteristic feature of angiosperm chloroplast genomes Streptocarpus and to conduct comparative analyses against [27], using GenBank genome fles. close relatives. Chloroplast genome sequence alignment was constructed using Mauve program [28] to check the gene order and 2. Materials and Methods sequence similarities/variations between 15 Lamiales cp genomes as in Tables 5 and 6. Nicotiana tabacum was added 2.1. Plant Material, DNA Extraction, Sequencing, and Assem- as reference genome (Figure 3) since it is considered to bly. Leaf samples were obtained from S. teitensis in Taita have the ideal angiosperm chloroplast genome structure. In hills,Kenya,andimmediatelydriedinsilicagel[22]to order to determine the phylogenetic position of Streptocarpus preserve until DNA extraction. Voucher herbarium spec- teitensis, the cp genome annotation information of the species imens (Voucher Number: SAJIT 006426) were deposited in Tables 5 and 6, together with two more Asterid species at the East Africa Herbarium (NMK) and Herbarium of (Sinadoxa corydalifolia and Cofea arabica)includedasout- Wuhan Botanical Garden (HIB) for future reference pur- groups, was obtained from the NCBI GenBank database. poses. Total genomic DNA of one individual was extracted However, in this analysis the species Cistanche deserticola from 100 mg of leaves via the MagicMag Genomic DNA was not used since it has been recorded to have lost all Micro Kit (Sangon Biotech Co., Shanghai, China) guided by the photosynthetic genes except psbM. A phylogenetic tree the manufacturer’s