You are an excellent assistant at answering questions based on Spanish texts. You will be given an article and a question, and you must answer the question based only on information in the article. The response should be extracted from the context verbatim.

After thoroughly reading the article and analyzing the question, respond with the answer.

Title:
Chloroplast

Context:
In cpDNA, there are several A → G deamination gradients. DNA becomes susceptible to deamination events when it is single stranded. When replication forks form, the strand not being copied is single stranded, and thus at risk for A → G deamination. Therefore, gradients in deamination indicate that replication forks were most likely present and the direction that they initially opened (the highest gradient is most likely nearest the start site because it was single stranded for the longest amount of time). This mechanism is still the leading theory today; however, a second theory suggests that most cpDNA is actually linear and replicates through homologous recombination. It further contends that only a minority of the genetic material is kept in circular chromosomes while the rest is in branched, linear, or other complex structures.

Question:
Where does the secondary theory say most genes are kept?

in branched, linear, or other complex structures