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，隶属核果木科Caryocaraceae）是一种广泛分布于巴西稀树草原的新热带乔木树种。该树种在巴西中部极具知名度，其果实常被用于当地特色料理，同时也是巴西本土植物中可快速纳入种植体系的候选物种之一。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，具备被子植物典型的四分体结构：包含两个拷贝的反向重复序列（IRa和IRb），每个长度为34902 bp，二者分别分隔开长度11852 bp的小单拷贝区（SSC）与长度84137 bp的大单拷贝区（LSC）。注释分析共鉴定出136个基因，其中包括87个蛋白编码基因、8个核糖体RNA（rRNA）基因与37个转运RNA（tRNA）基因。本研究共鉴定出49个重复DNA元件与85个微卫星位点。贝叶斯系统发育分析厘清了金虎尾目（Malpighiales）此前未解决的部分系统发育关系，将核果木科（Caryocaraceae）定为该目中一个独立的演化分支，且节点支持度极高。本研究整合了宝贵的科研信息，可为后续相关研究提供支撑，助力深入解析该类群的进化模式，并为未来的育种项目提供核心资源。