Complete chloroplast genome sequence of Caryocar brasiliense Camb. (Caryocaraceae) and comparative analysis brings new insights into the plastome evolution of Malpighiales

Abstract Caryocar brasiliense (Caryocaraceae) is a Neotropical tree species widely distributed in Brazilian Savannas. This species is very popular in central Brazil mainly by the use of its fruits in the local cuisine, and indeed it is one of the candidates, among Brazilian native plants, for fast track incorporation into cropping systems. Here we sequenced the complete chloroplast genome of C. brasiliense and used the data to access its genomic resources using high-throughput sequencing. The chloroplast exhibits a genome length of 165,793 bp and the typical angiosperm quadripartite structure with two copies of an inverted repeat sequence (IRa and IRb) of 34,902 bp each, separating a small single copy (SSC) region of 11,852 bp and a large single copy (LSC) region of 84,137 bp. The annotation analysis identified 136 genes being 87 protein-coding, eight rRNA and 37 tRNA genes. We identified 49 repetitive DNA elements and 85 microsatellites. A bayesian phylogenetic analysis helped to understand previously unresolved relationships in Malpighiales, placing Caryocaraceae as a separated group in the order, with high supported nodes. This study synthetizes valuable information for further studies allowing a better understanding of evolutionary patterns in the group and providing resources for future breeding programs.

摘要 巴西核果木（Caryocar brasiliense，核果木科Caryocaraceae）是一种新热带乔木树种，广泛分布于巴西塞拉多稀树草原。该物种在巴西中部广受欢迎，主要因其果实可用于当地特色烹饪；事实上，它是巴西本土植物中有望快速纳入种植系统的候选物种之一。
本研究通过高通量测序技术完成了巴西核果木的完整叶绿体基因组（chloroplast genome）测序，并利用该数据挖掘其基因组资源。该叶绿体基因组全长165793 bp，具备典型被子植物的四分体结构：包含两个反向重复序列（inverted repeat sequence，IRa与IRb）拷贝，每个长度为34902 bp，二者分别分隔出长单拷贝区（large single copy，LSC，84137 bp）与短小单拷贝区（small single copy，SSC，11852 bp）。
注释分析共鉴定出136个基因，其中87个为蛋白编码基因、8个核糖体RNA（rRNA）基因以及37个转运RNA（tRNA）基因。本研究共识别出49个重复DNA元件与85个微卫星序列。
贝叶斯系统发育分析（bayesian phylogenetic analysis）厘清了金虎尾目（Malpighiales）中此前未解决的类群关系，将核果木科确立为该目中一个独立分支，且节点支持度极高。
本研究提供的宝贵信息可为后续研究提供支撑，有助于进一步阐明该类群的演化模式，并为未来的育种项目提供相关资源。